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- PDB-2gzm: Crystal Structure of the Glutamate Racemase from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 2gzm
TitleCrystal Structure of the Glutamate Racemase from Bacillus anthracis
ComponentsGlutamate racemase
KeywordsISOMERASE / racemase / enzyme / glutamate
Function / homology
Function and homology information


glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
Glutamate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold ...Glutamate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-GLUTAMIC ACID / Glutamate racemase / Glutamate racemase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMay, M. / Santarsiero, B.D. / Johnson, M.E. / Mesecar, A.D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural and functional analysis of two glutamate racemase isozymes from Bacillus anthracis and implications for inhibitor design.
Authors: May, M. / Mehboob, S. / Mulhearn, D.C. / Wang, Z. / Yu, H. / Thatcher, G.R. / Santarsiero, B.D. / Johnson, M.E. / Mesecar, A.D.
History
DepositionMay 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate racemase
B: Glutamate racemase
C: Glutamate racemase
D: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,3268
Polymers118,7374
Non-polymers5894
Water8,899494
1
A: Glutamate racemase
B: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6634
Polymers59,3692
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glutamate racemase
D: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6634
Polymers59,3692
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint1 kcal/mol
Surface area20800 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint2 kcal/mol
Surface area40590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.346, 90.518, 116.799
Angle α, β, γ (deg.)90.000, 100.021, 90.000
Int Tables number4
Space group name H-MP1211
DetailsChains A and B form one dimer, and chains C and D form a second dimer.

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Components

#1: Protein
Glutamate racemase


Mass: 29684.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: racE-2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q81LA8, UniProt: A0A6L8PKK6*PLUS, glutamate racemase
#2: Chemical
ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein conc of 8 mG/mL, 50mM sodium glutamate, 2mM DTT, 5% PEG6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 77916 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 35.019 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.47
Reflection shellResolution: 1.99→2.11 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 31878 / Num. unique all: 10036 / Rsym value: 0.621 / % possible all: 91.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
SERGUIdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B74 fragments

1b74


Resolution: 1.99→20 Å / FOM work R set: 0.833 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3930 5 %random
Rwork0.203 ---
all0.203 77902 --
obs0.203 77902 98.4 %-
Solvent computationBsol: 70.207 Å2
Displacement parametersBiso mean: 40.226 Å2
Baniso -1Baniso -2Baniso -3
1--9.669 Å20 Å2-3.451 Å2
2---0.952 Å20 Å2
3---10.621 Å2
Refinement stepCycle: LAST / Resolution: 1.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8353 0 40 494 8887
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.99-20.333140.415632646
2-2.020.424720.38612541326
2.02-2.030.368760.33814431519
2.03-2.050.366620.3215341596
2.05-2.060.334820.31514911573
2.06-2.080.358820.31714671549
2.08-2.090.2831000.29515211621
2.09-2.110.301660.26514771543
2.11-2.130.294850.27514931578
2.13-2.140.254610.24914981559
2.14-2.160.304840.27315411625
2.16-2.180.308820.25814661548
2.18-2.20.265760.24214951571
2.2-2.220.279930.23915041597
2.22-2.240.26870.24314741561
2.24-2.260.297830.24215101593
2.26-2.290.288690.24914911560
2.29-2.310.225880.22315051593
2.31-2.330.275720.2215151587
2.33-2.360.266750.20815051580
2.36-2.390.249750.20314721547
2.39-2.410.27830.22714941577
2.41-2.440.258760.20715141590
2.44-2.470.272860.20214981584
2.47-2.510.198910.18414971588
2.51-2.540.247950.18114881583
2.54-2.580.216750.18415131588
2.58-2.620.278790.21114571536
2.62-2.660.247770.19415351612
2.66-2.70.217830.17514821565
2.7-2.750.261830.17915211604
2.75-2.80.21630.18415121575
2.8-2.850.229850.18914851570
2.85-2.910.237690.19114991568
2.91-2.970.238790.1815161595
2.97-3.040.254780.18314841562
3.04-3.110.248750.19315401615
3.11-3.20.248750.18914921567
3.2-3.290.241910.1914971588
3.29-3.40.232840.16714871571
3.4-3.520.213900.17515331623
3.52-3.660.206680.17614811549
3.66-3.820.234800.1815061586
3.82-4.020.237750.17715471622
4.02-4.270.249790.17814991578
4.27-4.60.203810.17915041585
4.6-5.060.23940.18415161610
5.06-5.770.257950.25214871582
5.77-7.220.235730.23815441617
7.22-200.164840.17315561640
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4cis_peptide.param
X-RAY DIFFRACTION5dgl.param

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