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

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Basic information

Entry
Database: PDB / ID: 2jfu
TitleCrystal structure of Enterococcus faecium glutamate racemase in complex with phosphate
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
PHOSPHATE ION / Glutamate racemase
Similarity search - Component
Biological speciesENTEROCOCCUS FAECIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1May 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)31,8543
Polymers31,6641
Non-polymers1902
Water4,486249
1
A: GLUTAMATE RACEMASE
hetero molecules

A: GLUTAMATE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7096
Polymers63,3292
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)85.960, 85.960, 92.300
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 / Fragment: RESIDUES 4-277
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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 100 MM SODIUM CITRATE PH 5.6, 0.6-0.8M AMMONIUM SULPHATE AND 30% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.8→34 Å / Num. obs: 36792 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 19.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 98.6

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Processing

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

2jfo


Resolution: 1.8→34 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 3431 9.3 %RANDOM
Rwork0.1927 ---
obs-36792 --
Solvent computationBsol: 51.0572 Å2 / ksol: 0.413381 e/Å3
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.859 Å2-1.726 Å20 Å2
2---1.859 Å20 Å2
3---3.718 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 10 249 2328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004885
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_deg1.2932
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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