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- PDB-2vvt: Glutamate Racemase (MurI) from E. faecalis in complex with a 9-Be... -

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Basic information

Entry
Database: PDB / ID: 2vvt
TitleGlutamate Racemase (MurI) from E. faecalis in complex with a 9-Benzyl Purine inhibitor
ComponentsGLUTAMATE RACEMASE
KeywordsISOMERASE / GLUTAMATE RACEMASE / PEPTIDOGLYCAN SYNTHESIS / CELL WALL BIOGENESIS/DEGRADATION / CELL SHAPE / BENZYL PURINE / MURI INHIBITOR
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 / Chem-I24 / Glutamate racemase
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGeng, B. / Breault, G. / Comita-Prevoir, J. / Petrichko, R. / Eyermann, C. / Lundqvist, T. / Doig, P. / Gorseth, E. / Noonan, B.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Exploring 9-Benzyl Purines as Inhibitors of Glutamate Racemase (Muri) in Gram-Positive Bacteria.
Authors: Geng, B. / Breault, G. / Comita-Prevoir, J. / Petrichko, R. / Eyermann, C. / Lundqvist, T. / Doig, P. / Gorseth, E. / Noonan, B.
History
DepositionJun 11, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,6846
Polymers62,4962
Non-polymers1,1874
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-8.2 kcal/mol
Surface area26320 Å2
MethodPQS
Unit cell
Length a, b, c (Å)44.402, 69.432, 165.120
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: 31248.240 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-270
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-I24 / 2-butoxy-9-(2,6-difluorobenzyl)-N-(2-morpholin-4-ylethyl)-9H-purin-6-amine


Mass: 446.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28F2N6O2
#3: Chemical ChemComp-DGL / D-GLUTAMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 703 / 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 137 AND 144 (THR AND ASP IN NP_814851)

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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 Å3/Da / Density % sol: 39 % / Description: NONE
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 3350, 100 MM TRIS PH 7.5, 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9757
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 1.65→81.65 Å / Num. obs: 205055 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.6
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JFO

2jfo


Resolution: 1.65→81.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.502 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 3003 5.1 %RANDOM
Rwork0.15 ---
obs0.152 56198 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.49 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.65→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 84 703 4836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224209
X-RAY DIFFRACTIONr_bond_other_d0.0010.022760
X-RAY DIFFRACTIONr_angle_refined_deg1.4612.0065715
X-RAY DIFFRACTIONr_angle_other_deg0.9236841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3865532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.77125142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15915731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6861515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02721
X-RAY DIFFRACTIONr_nbd_refined0.2270.2972
X-RAY DIFFRACTIONr_nbd_other0.1960.22965
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22103
X-RAY DIFFRACTIONr_nbtor_other0.0870.22060
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2474
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.268
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0471.52784
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47524330
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.42631659
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6944.51385
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.207 254
Rwork0.155 4121

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