[English] 日本語
Yorodumi
- PDB-2gzm: Crystal Structure of the Glutamate Racemase from Bacillus anthracis -

+
Open data


ID or keywords:

Loading...

-
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 2 / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / 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 2 / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more