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- PDB-2jfw: Crystal structure of Enterococcus faecium glutamate racemase in c... -

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Basic information

Entry
Database: PDB / ID: 2jfw
TitleCrystal structure of Enterococcus faecium glutamate racemase in complex with tartrate
ComponentsGLUTAMATE RACEMASE
KeywordsISOMERASE / PEPTIDOGLYCAN BIOSYNTHESIS / GLUTAMATE RACEMASE
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
L(+)-TARTARIC ACID / Glutamate racemase
Similarity search - Component
Biological speciesENTEROCOCCUS FAECIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8152
Polymers31,6641
Non-polymers1501
Water4,342241
1
A: GLUTAMATE RACEMASE
hetero molecules

A: GLUTAMATE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6294
Polymers63,3292
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2490 Å2
ΔGint-12.6 kcal/mol
Surface area26520 Å2
MethodPQS
Unit cell
Length a, b, c (Å)85.423, 85.423, 93.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein GLUTAMATE RACEMASE


Mass: 31664.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECIUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3XZW8, glutamate racemase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growDetails: PROTEIN FORMULATED AT 10 MG/ML WITH 200MM AMMONIUM ACETATE PH 7.4, 5MM D-L GLUTAMATE, 1 MM TCEP AND CRYSTALLISED WITH 200 MM DI-SODIUM TATRATE AND 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: May 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→22 Å / Num. obs: 25692 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.7 / % possible all: 78.7

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Processing

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

2jfu


Resolution: 2→22 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 1309 4.8 %RANDOM
Rwork0.2036 ---
obs-25682 --
Solvent computationBsol: 65.9739 Å2 / ksol: 0.369591 e/Å3
Displacement parametersBiso mean: 40.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.225 Å2-0.42 Å20 Å2
2---1.225 Å20 Å2
3---2.45 Å2
Refinement stepCycle: LAST / Resolution: 2→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 10 241 2316
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.056
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_deg1.33
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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