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- PDB-2jfq: Crystal structure of Staphylococcus aureus glutamate racemase in ... -

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Basic information

Entry
Database: PDB / ID: 2jfq
TitleCrystal structure of Staphylococcus aureus glutamate racemase in complex with D- Glutamate
ComponentsGLUTAMATE RACEMASE
KeywordsISOMERASE / CELL WALL / CELL SHAPE / GLUTAMATE RACEMASE / PEPTIDOGLYCAN SYNTHESIS / PEPTIDOGLYCAN BIOSYNTHESIS
Function / homology
Function and homology information


glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / identical protein binding
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
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLundqvist, T.
CitationJournal: Nature / Year: 2007
Title: Exploitation of Structural and Regulatory Diversity in Glutamate Racemases
Authors: Lundqvist, T. / Fisher, S.L. / Kern, G. / Folmer, R.H.A. / Xue, Y. / Newton, D.T. / Keating, T.A. / Alm, R.A. / De Jonge, B.L.M.
History
DepositionFeb 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE RACEMASE
B: GLUTAMATE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0934
Polymers63,7992
Non-polymers2942
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-9.7 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.430, 88.870, 96.560
Angle α, β, γ (deg.)90.00, 109.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GLUTAMATE RACEMASE


Mass: 31899.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6GHT5, glutamate racemase
#2: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPATENT DATABASE Q6GHT5. CLOSEST PUBLIC DATABASE REFERENCE SWISS-PROT MURI_STAAR WITH PRO AT ...PATENT DATABASE Q6GHT5. CLOSEST PUBLIC DATABASE REFERENCE SWISS-PROT MURI_STAAR WITH PRO AT POSITION 110. THIS SEQUENCE DIFFERENCE TO THE SITED PUBLIC DATA BASE IS REAL AND CORRESPONDS TO A DIFFERENCE BETWEEN DIFFERENT STRAINS OF THE BACTERIA

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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: 3 Å3/Da / Density % sol: 59 %
Crystal growpH: 7.4
Details: PROTEIN FORMULATED AT 10 MG/ML WITH 200 MM AMMONIUM ACETATE PH 7.4, 5 MM D-L GLUTAMATE, 1 MM TCEP AND CRYSTALLISED WITH 0.17 MM AMMONIUM SULPHATE AND 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9392
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 2.13→34 Å / Num. obs: 41628 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.7
Reflection shellResolution: 2.13→2.22 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 90.7

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Processing

Software
NameVersionClassification
CNX2000.2refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JFP

2jfp


Resolution: 2.15→34 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2103 5 %RANDOM
Rwork0.202 ---
obs-41628 --
Solvent computationBsol: 47.6611 Å2 / ksol: 0.412448 e/Å3
Displacement parametersBiso mean: 27.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.867 Å20 Å2-1.673 Å2
2---3.991 Å20 Å2
3---2.124 Å2
Refinement stepCycle: LAST / Resolution: 2.15→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4160 0 20 133 4313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005627
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.19107
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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