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§1§ Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein
and member of the highly conserved YjgF family §1§
1. [16]Sangita Sinha [17]*,
2. [18]Pekka Rappu [19]†,
3. [20]S. C. Lange [21]*,
4. [22]Pekka Mäntsälä [23]†,
5. [24]Howard Zalkin [25]‡, and
6. [26]Janet L. Smith [27]* , [28]§
1.
Departments of ^*Biological Sciences and ^‡Biochemistry, Purdue
University, West Lafayette, IN 47907; and ^†Department of
Biochemistry and Food Chemistry, University of Turku, Vatselankatu 2,
FIN-20014 Turku, Finland
1. Communicated by Michael G. Rossmann, Purdue University, West
Lafayette, IN (received for review July 15, 1999)
[29]Next Section
§2§ Abstract §2§
The yabJ gene in Bacillus subtilis is required for adenine-mediated
repression of purine biosynthetic genes in vivo and codes for an
acid-soluble, 14-kDa protein. The molecular mechanism of YabJ is
unknown. YabJ is a member of a large, widely distributed family of
proteins of unknown biochemical function. The 1.7-Å crystal structure
of YabJ reveals a trimeric organization with extensive buried
hydrophobic surface and an internal water-filled cavity. The most
important finding in the structure is a deep, narrow cleft between
subunits lined with nine side chains that are invariant among the 25
most similar homologs. This conserved site is proposed to be a binding
or catalytic site for a ligand or substrate that is common to YabJ and
other members of the YER057c/YjgF/UK114 family of proteins.
Purine biosynthesis in Bacillus subtilis is regulated by the purine
operon repressor gene, purR. The purR operon consists of purR and yabJ,
an ORF of unknown function. The repressor PurR binds to control regions
upstream of the transcription start sites and regulates transcription
of purEKBC(orf)QLFMNHD in the pur operon, of purR and yabJ in the purR
operon, and of purA ([30]1). PurR binding to control-site DNA is
blocked by 5-phosphoribosyl-1-pyrophosphate (PRPP), a central
nucleotide metabolite that acts as an inducer of pur operon and purA
transcription. 5-phosphoribosyl-1-pyrophosphate is the starting
material for purine biosynthesis. No other metabolite, nucleotide,
nucleoside, or nucleotide base is known to affect PurR DNA binding in
vitro ([31]2).
Recently, yabJ, the distal coding sequence in the purR operon, was
shown to affect PurR function in vivo ([32]3). Regulation of
transcription of purine biosynthetic genes is sensitive to levels of
some nutrients and depends on the interrelated pools of
5-phosphoribosyl-1-pyrophosphate, nucleotides, nucleosides, and
nucleotide bases. Adenine uptake by B. subtilis indirectly increases
PurR repression of pur operon and purA transcription through changes to
the 5-phosphoribosyl-1-pyrophosphate pool. YabJ is also required for
adenine-mediated repression of purA in vivo ([33]3). The mechanism by
which YabJ stimulates adenine-mediated repression of purA by PurR is
unknown. However, YabJ and PurR may be cotranslated and produced in
stoichiometric quantities in vivo because the last codon of purR
overlaps the initiation codon of yabJ.
YabJ belongs to a widely distributed family of proteins of unknown
function. Members of the YER057c/YjgF/UK114 family of proteins are
identified by sequence similarity, having 20–98% pairwise identity. The
family is named for genes or proteins in yeast (YER057c), Escherichia
coli (yjgF), and goat (UK114). All are ≈14-kDa proteins and do not
occur as domains of larger proteins. Many YjgF proteins are
acid-soluble. A variety of biological processes have been reported to
be influenced by YjgF proteins, in addition to the YabJ function in
purine regulation. Homologs occur in bacteria, animals, and fungi but
are absent from the genomes of most archaea and of several parasitic
prokaryotes that also lack many biosynthetic pathways. No YjgF homolog
has yet been detected in a plant, although its presence in a
cyanobacterium ([34]4) suggests that it may also occur in plants. No
three-dimensional structures of YjgF proteins have been published,
although crystallization of a rat homolog has been reported ([35]5).
Here we present the 1.7-Å crystal structure of B. subtilis YabJ. The
structure reveals a conserved cleft on the protein surface that will
aid in elucidation of a function for this family of proteins.
[36]Previous Section[37]Next Section
§2§ Materials and Methods §2§
§3§ Cloning and Overexpression of yabJ. §3§
The yabJ gene was amplified by PCR from chromosomal DNA of a wild-type
B. subtilis strain. The 446-bp PCR product was confirmed by sequencing
and was cloned into a T7 expression vector to produce plasmid pDR1. E.
coli strain BL21(DE3)/pLysS was transformed with pDR1. Strain
BL21(DE3)/pLysS/pDR1 was grown at 37°C in LB medium supplemented with
100 μg/ml ampicillin to an OD[600] of 0.6, was induced with 0.4 mM
isopropyl β-d-thiogalactoside, and was grown for 10 hr at 30°C. Cells
were harvested by centrifugation and were resuspended in 50 mM Tris⋅HCl
(pH 8.0), 2 mM EDTA, 10 mM MgCl[2], and 10 μg/ml DNase I (5 ml of
buffer per gram of wet cells). The cell pellet was frozen at −20°C.
§3§ Purification of YabJ. §3§
Frozen BL21(DE3)/pLysS/pDR1 cells were thawed and incubated at room
temperature for 15 min. The lysate was clarified by centrifugation at
20,000 × g for 30 min. All purification steps were performed at room
temperature. The lysate soluble fraction was stirred during addition of
70% perchloric acid to a final concentration of 5%. Precipitated
proteins were removed by centrifugation at 12,000 × g for 15 min. The
perchloric acid extract was neutralized with 1.5 volumes of 1 M
Tris⋅HCl (pH 8.0), and the extract was dialyzed against Buffer A (40 mM
sodium phosphate buffer, pH 7.4). The ≈95% pure YabJ sample was
chromatographed by using the resin Poros HQ/M (PerSeptive Biosystems,
Framingham, MA). The column was washed with 5 volumes of Buffer A. YabJ
was eluted with 0.2 M NaCl, was dialyzed against Buffer A, and was
concentrated by ultrafiltration. N-terminal sequence analysis showed
that Met1 was not present in the purified protein. The protein was
stored at 4°C or was frozen in small aliquots for long-term storage at
−70°C. The overall yield was 120 mg of purified YabJ per liter of E.
coli culture.
§3§ Crystallization and Data Collection. §3§
YabJ was crystallized by hanging-drop vapor diffusion from a 1:1
mixture of protein (6.3 mg/ml YabJ in Buffer A) and reservoir (20%
polyethylene glycol 4,000/0.45 M ammonium acetate/0.1 M sodium acetate,
pH 4.6) solutions. Crystals grew to a maximum size of ≈0.1 × 0.1 × 0.6
mm in 4–5 days and were stabilized in reservoir solution. A Hg
derivative was prepared by soaking for 3 hr in 0.5 mM ethyl Hg
phosphate in reservoir solution, followed by back soaking for 0.5 hr.
Crystals were cryoprotected by a 3-min soak in 15% polyethylene glycol
400 in reservoir solution and were flash-frozen in a N[2] cold stream
at 100 K. Unit cell parameters in space group P6[5] are a = b = 53.3 Å
and c = 204.9 Å, which is consistent with either two (V [m] = 3.1
Å^3/Da, ≈60% solvent) or three (V [m] = 2.0 Å^3/Da, ≈40% solvent)
copies of the YabJ polypeptide per asymmetric unit. All data used for
structure determination and refinement were collected from a single,
Hg-derivatized, frozen crystal. Multiwavelength anomalous diffraction
(MAD) data were collected at BioCARS beam line BM14D at the Advanced
Photon Source (Argonne National Laboratory). MAD data (λ[1], λ[2],
λ[3]; Table [38]1) were recorded on an Q1 CCD detector (Area Detector
Systems, Poway, Ca) as two 80° sweeps of data at each wavelength.
Resolution was limited by detector size and the 205-Å c axis, resulting
in incomplete coverage of reciprocal space at the detector edge.
Several weeks later, complete, high resolution, 1.7-Å data (λ[4], Table
[39]1) were collected from the same crystal by using BioCARS beam line
BM14C at the Advanced Photon Source. The data were recorded on a Mar
345 imaging plate detector (X-ray Research GmbH, Hamburg, Germany) as a
single, 80° sweep of data. Data integration and reduction were done by
using the hkl package ([40]6). The MAD data set used for phasing was
produced by scaling the λ[1], λ[2], and λ[4] data sets to the merged
data for λ[3], using scaleit from the CCP4 suite ([41]7). For phase and
model refinement, a complete high-resolution data set (λ[3] + λ[4],
Table [42]1) was generated by merging data at λ[3] (30–2.5 Å) and λ[4]
(3–1.7 Å).
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Table 1
Crystallographic summary
§3§ Structure Determination and Refinement. §3§
Positions of three Hg atoms were determined by inspection of a Bijvoet
difference Patterson map using the λ[2] data set. Refinement of the Hg
partial structure and MAD phasing were performed by the
pseudo-isomorphous replacement approach using mlphare ([45]8).
Noncrystallographic 3-fold symmetry was clearly visible in the
unmodified MAD map at 2.7-Å resolution. A C3 noncrystallographic
symmetry operator was located and refined by using ncs6d ([46]9).
Phases were refined and extended to 2.0 Å by 3-fold averaging,
histogram matching, and solvent flattening with a 32% solvent mask
using dm ([47]10) and the λ[3] + λ[4] data set. The overall figure of
merit for all reflections to 2.0 Å was 0.63.
All model building was done in the program o ([48]11). The model was
refined against the λ[3] + λ[4] data set using maximum likelihood
amplitude and phase probability targets using cns ([49]12). The initial
model had R [work] = 0.355 and R [free] = 0.351 for all data between
30.0 and 2.0 Å. During the initial cycles of refinement, the model was
restrained by 3-fold noncrystallographic symmetry. The last iteration
of refinement and model building was followed by one round of atomic
occupancy refinement for residues in dual positions and for the ethyl
Hg ions. Final R [work] = 0.166 and R [free] = 0.197 for all data
between 30.0 and 1.7 Å. The model, including 124 residues in each of
three YabJ monomers, one ethyl Hg ion covalently linked to Cys104 in
each of two monomers, two partially occupied Hg sites in the third
monomer, six acetate ions, and 474 water molecules, has been deposited
in the Protein Data Bank and is available with ID code [50]1qd9. A
crystallographic summary is presented in Table [51]1.
[52]Previous Section[53]Next Section
§2§ Results and Discussion §2§
§3§ Protein Production and Structure Determination. §3§
B. subtilis YabJ was readily produced in E. coli from an inducible
plasmid. Purification was simplified by the acid extraction step. We
tried this approach because several YabJ homologs were reported to be
acid stable ([54]13, [55]14), and acid solubility was exploited in the
purification of the rat homolog ([56]15), which is 45% identical to
YabJ. The crystal structure was determined by Hg MAD, based on
modification of the single cysteine residue in YabJ. A complete,
high-quality model of YabJ resulted from refinement against complete
1.7-Å data. Electron density is clear for all parts of the protein. The
model agrees well with the diffraction data and with stereochemical
criteria (Table [57]1). No residues are in forbidden regions of the
Ramachandran plot ([58]16). The estimated coordinate error of the final
model is 0.19 Å ([59]17).
§3§ Protein Structure. §3§
The YabJ monomer is a 124-residue polypeptide folded into a single
domain. The YabJ fold is a six-stranded, mostly antiparallel β-sheet
with one parallel connection (Fig. [60]1). Two α-helices pack against
one face of the β-sheet. The core of each monomer includes no ionizable
groups or polar side-chain interactions. This structural feature may
contribute to the acid stability of YabJ. Preliminary refinement of the
YabJ model against data from Hg-free crystals at pH 6.5 indicates no
significant structural change from the Hg complex at pH 4.6 apart from
rotation of the Cys104 side chain from χ[1] = 180° to χ[1] = −60°.
[61]Figure 1
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Figure 1
Stereo view of the YabJ monomer. The ribbon diagram is rendered in
rainbow colors from blue at the N terminus to red at the C-terminus.
The figure was produced with molscript ([65]31) and raster3d ([66]32).
YabJ is a symmetric trimer in crystals (Fig. [67]2). The three β-sheets
of the trimer form a triangular barrel, with the β-strands
approximately parallel to the barrel 3-fold axis. The six α-helices of
the trimer pack on the outside of the barrel. Residues in strands β3–β6
of each monomer participate in the trimer interface, which is
constructed of alternating hydrophobic and polar regions. At the top of
the barrel, the three backbones form a ring of nine intersubunit
hydrogen bonds involving residues 106, 108, and 109. Below this polar
region is an extensive hydrophobic interface including six residues
from each monomer (Phe77, Met81, Val105, Val107, Leu110, Pro111). In
the center of the trimer is a polar cavity filled with 21 ordered water
molecules and ringed with six intersubunit polar contacts, consisting
of a salt bridge from Lys73 (β4) and a hydrogen bond from Ser103 (β5)
in each monomer to Glu119 (β6) in an adjacent monomer. Each water
molecule in the cavity forms at least three hydrogen bonds to other
waters or to protein atoms (Tyr28, Ser29, Lys73, Thr75, Glu119,
Val120), and the constellation of 21 waters has ≈3-fold symmetry.
Another 12 intersubunit hydrogen bonds are formed by nearby residues
(Ser18, Ser30, and Gly31 with Lys99, Pro100, and Arg102). The floor of
the polar cavity is formed by three Tyr28 (β3) side chains, which are
hydrogen-bonded to a cavity water molecule. The cavity waters would be
accessible to external bulk solvent by slight conformational breathing
of the Tyr28 side chains. The Tyr28 residues are the beginning of
another hydrophobic interface, which includes eight residues from each
monomer (Ile21, Val23, Met26, Tyr28, Val72, Ala101, Ile121, Leu123). At
the bottom of the barrel is a ring of six hydrogen bonds between the
amides of Asn24 and Asn25 in adjacent subunits.
[68]Figure 2
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Figure 2
YabJ Trimer. Subunits are rendered in different colors in this ribbon
diagram viewed along the molecular threefold axis. The position of the
Hg ion used to solve the structure and bound to Cys104 is indicated
with a sphere.
The YabJ quaternary structure has not been established in solution.
Several features of the crystalline trimer, including the extent and
character of buried monomer surface and the dehydration of subunit
interfaces, are consistent with a YabJ trimer in solution. The total
monomer-accessible surface buried in the trimer is very large, a total
of 1,850 Å^2, ≈28% of the total ([72]18). Two extensive hydrophobic
contact regions are part of the trimeric aggregate. Apart from the
central cavity described above, the subunit interfaces do not bury any
water molecules. Thus, the subunit interfaces of the crystalline trimer
are much more like biological aggregates than like crystal contacts,
which are extensively hydrated, rather small and very polar. Some YabJ
homologs have been reported to be dimeric ([73]13, [74]19, [75]20,
[76]29). However, residues forming the polar and hydrophobic zones of
the subunit interface are very well conserved among the YabJ homologs,
suggesting that all are trimers.
Neighboring subunits of the trimer create three clefts on the outer
surface of YabJ. The clefts are narrow (8–9 Å) and deep (12–13 Å).
Glu117 forms the innermost surface of each cleft, and several
hydrophobic side chains ring the outermost surface.
§3§ YabJ in the purR operon of B. subtilis. §3§
Transcription of purA is repressed ≈10-fold in vivo by addition of
adenine to cells ([77]3). This repression is mediated by PurR. However,
disruption of YabJ results in the loss of adenine-mediated PurR
repression by an unknown mechanism. The predominance of acidic residues
on the surface of YabJ (calculated pI = 5.3) suggests that it does not
interact directly with DNA. Preliminary soaking experiments with YabJ
crystals and various purine-containing molecules and calcium ions,
which are reported to bind a YabJ homolog ([78]20), have not resulted
in binding in the cleft or anywhere else on YabJ. Further experiments
are underway to identify a ligand or substrate.
§3§ Stuctural Homolog. §3§
YabJ has no detectable sequence similarity to any other protein in the
structure database ([79]21). Unexpectedly, it has a fold ([80]22) and
aggregation state in common with chorismate mutase from B. subtilis
([81]23). The core fold, β3–β6 and α1, is present in both structures.
The second α-helix of YabJ is replaced by a shorter 3[10]-helix in
chorismate mutase. Strands β1 and β2 of YabJ and a fifth, C-terminal
strand of chorismate mutase lie on the same end of the core β-sheet but
are not superimposable. Based on the structure alignment, the sequences
of YabJ and chorismate mutase are only 8% identical. The rmsd for the
83 superimposable C[α] atoms per monomer is 2.6 Å (Fig. [82]3 A). YabJ
and chorismate mutase also form very similar trimers with an rmsd of
3.3 Å for 249 C[α] atoms. However, the trimer interface of chorismate
mutase is entirely hydrophobic and lacks the polar central cavity of
YabJ.
[83]Figure 3
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Figure 3
Comparison of YabJ and B. subtilis chorismate mutase. (A) Superposition
of subunits. C[α] traces of YabJ (thick lines) and chorismate mutase
(thin lines) are overlaid. Orientation is similar to Fig. [87]1. (B)
Ribbon diagram of the chorismate mutase trimer. The reaction product
prephenate is shown in the active site cleft. Orientation is as in Fig.
[88]2.
Chorismate mutase catalyses the unimolecular, pericyclic rearrangement
of chorismate to prephenate, a reaction at the branch point of the
biosynthetic pathway for aromatic amino acids. The three active sites
of the chorismate mutase trimer are located in clefts between subunits,
analogous to the clefts at the subunit interfaces of the YabJ trimer
(Fig. [89]3 B). Eleven residues in the active site of chorismate mutase
have been implicated in substrate binding and transition state
stabilization ([90]23). Two of these side chains, Phe 57 and Cys 75,
have chemical and topological equivalents, Phe 84 and Cys 104, in YabJ.
However, elsewhere in the cleft, YabJ and chorismate mutase do not have
common functional groups. We conclude that YabJ and chorismate mutase
probably have a common ancestor but have evolved to perform different
functions.
§3§ Sequence Homologs. §3§
YabJ belongs to the YER057c/YjgF/UK114 family of small proteins
(ProSite accession nos. PS01094 and UPF0076). We identified a total of
37 homologs having 20–53% sequence identity with YabJ in the sequence
database ([91]21). This level of identity indicates a common ancestor,
a common fold, and possibly a common function for the proteins.
No invariant residues result from multiple alignment ([92]24) of the 38
sequences of YabJ and its homologs. However, if the homologs have
evolved to more than one function, invariance would not be expected. To
probe the sequence data for clues to biochemical function, we looked
for a subset of more closely related sequences. Based on the multiple
sequence alignment, the homologs were divided into two groups—a “high
identity” group of 25 more closely related sequences, each having at
least 43% identity with another sequence in the group, and a “low
identity” group of 13 more divergent sequences, each having generally
<30% identity to any member of either group. The high-identity group,
including YabJ, has nine invariant residues (Fig. [93]4). Although they
are spread throughout the primary sequence, all of these residues map
to the narrow, deep cleft between subunits of the YabJ trimer (Fig.
[94]5). This site is structurally analogous to the active site of
chorismate mutase. The clustering of invariant residues in the cleft
strongly suggests a common molecular function of catalysis or binding
for members of the high-identity group.
[95]Figure 4
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Figure 4
Comparison of sequences of YabJ and 24 homologs in the high-identity
group. Residues in red boxes are invariant; in yellow boxes are sites
of conservative substitution. Secondary structures are indicated above
the alignment. Residues in the subunit interface are indicated by
triangles below the alignment, and those with main-chain interactions
by circles. Multiple sequence alignment was done with clustalw
([99]24). The figure was produced with alscript ([100]33).
[101]Figure 5
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Figure 5
Stereo view of the intersubunit cleft of YabJ. The translucent
molecular surface is in gray, with surfaces of invariant residues from
the two subunits in rust and cyan. C[α] wire diagrams for two subunits
are yellow and white, as are the side chains of invariant residues
(Phe84, Asn88, and Arg102 in the yellow subunit, and Pro11, Tyr17,
Gly31, Asn56, Pro111, and Glu117 in the white subunit). The figure was
produced with dino (ref. [105]34;
[106]http://www.bioz.unibas.ch/∼x-ray/dino).
Two structural databases were queried for similar residue
constellations in YabJ and any protein of known structure and function.
procat ([107]25) is a database of functional groups in enzyme active
sites. None of these active site templates matches any constellation of
residues in the YabJ structure. Conversely, the nine YabJ side chains
that are invariant in the high-identity group do not have an analog
among protein structures deposited in the Protein Data Bank, as probed
with the program spasm ([108]26). Thus, it appears that the arrangement
of residues in the conserved cleft of YabJ does not exist in any
reported protein structure.
Biological functions attributed to YabJ homologs do not point to a
common biochemical activity. Most of the homologs are hypothetical
proteins of unknown function. The genetic context of yabJ (purR operon)
correlates with the observed phenotype of yabJ ^− (loss of purA
repression by adenine). Similarly, Lactococcus lactis aldR has been
implicated in regulation of isoleucine biosynthesis ([109]27).
Salmonella typhimurium yjgF may have a role in regulation of the
isoleucine and thiamine biosynthetic pathways ([110]28). In cases in
which protein products have been studied, no certain biochemical
activity has been identified, and a wide variety of biological
functions has been proposed. The rat and human homologs are putative
translation inhibitors ([111]14, [112]29), goat UK114 is implicated in
tumor antigenicity ([113]30), mouse Hrp12 is thought to be a heat
response protein ([114]19), and the bovine and rat homologs are
proposed to affect activation of the calcium-dependent protease calpain
([115]20). Sequences for all of these homologs are in the high-identity
group. The strong conservation of side chains in the YabJ cleft implies
that the homologs of the high-identity group achieve their variety of
biological functions by a common biochemical mechanism.
Any common biochemical mechanism for the broadly distributed YabJ
homologs would necessarily involve ligand or substrate binding to the
12-Å deep, 8-Å wide conserved cleft at the subunit interface (Fig.
[116]5). We screened broadly for a small-molecule ligand by soaking
crystals at neutral pH in a stabilizing solution augmented with B.
subtilis cell extract. No electron density for a ligand was identified
in difference electron density maps computed by using diffraction data
from the soaked crystals. This negative result does not distract us
from investigation of the conserved cleft. Studies are underway to
identify a ligand or substrate in solution and in vivo.
We propose that YabJ and the high-identity homologs use the conserved,
deep, narrow cleft for catalysis or binding of a common chemical
entity. Molecular mechanisms by which these proteins could use a common
biochemistry to influence a variety of biological processes include,
among others, binding a regulatory macromolecule, altering the
concentration of a key small-molecule metabolite through catalysis, and
binding another macromolecule after a ligand-induced conformational
change. Use of the conserved, deep, narrow cleft for binding implies
recognition of an appropriately shaped small-molecule ligand or a
single amino acid residue in a protein ligand. The structure of YabJ
should be an important guide for identification of this molecule. This
work also illustrates the challenges of deducing protein function from
sequence and three-dimensional structure.
[117]Previous Section[118]Next Section
§2§ Acknowledgments §2§
The authors thank the staff of BioCARS at the Advanced Photon Source,
Argonne National Laboratory, for their advice during the data
collection and Carol Greski for expert preparation of the manuscript.
This work was supported by National Institutes of Health Grants
DK-42303 to J.L.S. and GM-24658 to H.Z. and by the Finnish Ministry of
Education (P.M.).
[119]Previous Section[120]Next Section
§2§ Note §2§
After completion of this manuscript, a structure of E. coli YjgF, a
YabJ homolog, was presented at the annual meeting of the American
Crystallographic Association ([121]35). The function of E. coli YjgF is
unknown. In E. coli, yjgF is not linked to purR, and E. coli purR is
unrelated to B. subtilis purR.
[122]Previous Section[123]Next Section
§2§ Footnotes §2§
* [124]↵ § To whom reprint requests should be addressed. E-mail:
smithj{at}purdue.edu.
* Data deposition: The atomic coordinate has been deposited in the
Protein Data Bank, [125]www.rcsb.org (PDB ID code [126]1qd9).
* Abbreviation:
rmsd,
rms deviation
* Copyright © 1999, The National Academy of Sciences
[127]Previous Section
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