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- PDB-2jfo: Crystal structure of Enterococcus faecalis glutamate racemase in ... -

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Basic information

Entry
Database: PDB / ID: 2jfo
TitleCrystal structure of Enterococcus faecalis glutamate racemase in complex with D- and L-Glutamate
ComponentsGLUTAMATE RACEMASE
KeywordsISOMERASE / GLUTAMATE RACEMASE / 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 / GLUTAMIC ACID / Glutamate racemase
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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 3, 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 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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
B: GLUTAMATE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5074
Polymers63,2132
Non-polymers2942
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.290, 82.080, 111.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUTAMATE RACEMASE


Mass: 31606.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q836J0, glutamate racemase
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDATABASE REFERENCE GENESEQP ADR04180 (PATENT DATABASE). CLOSEST PUBLIC REFERENCE IS GENPEPT NP_ ...DATABASE REFERENCE GENESEQP ADR04180 (PATENT DATABASE). CLOSEST PUBLIC REFERENCE IS GENPEPT NP_814851 HAS 2 DIFFERENCES AT RESIDUE 157 AND 164 (THR AND ASP IN NP_814851). THESE ARE TRUE DIFFERENCES CORRESPONDING TO DIFFERENCES BETWEEN DIFFERENT STRAINS OF 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: 2.4 Å3/Da / Density % sol: 43.5 %
Crystal growpH: 7.5
Details: PROTEIN FORMULATED AT 10 MG/ML WITH 200MM AMMONIUM ACETATE PH 7.4, 5MM D-L GLUTAMATE, 1 MM TCEP AND CRYSTALLISED WITH 0.2 MM MGCL2 AND 20-25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9184 , 0.9786 , 0.9789 , 0.9184
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.97861
30.97891
ReflectionResolution: 2.5→20 Å / Num. obs: 18738 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 96.2

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Processing

Software
NameVersionClassification
CNX2002.2refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 960 4.9 %RANDOM
Rwork0.2043 ---
obs-18738 --
Solvent computationBsol: 38.4821 Å2 / ksol: 0.354432 e/Å3
Displacement parametersBiso mean: 38.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.216 Å20 Å20 Å2
2---1.422 Å20 Å2
3---0.207 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 20 184 4244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008049
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_deg1.26972
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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