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- PDB-2oho: Structural Basis for Glutamate Racemase Inhibitor -

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Basic information

Entry
Database: PDB / ID: 2oho
TitleStructural Basis for Glutamate Racemase Inhibitor
ComponentsGlutamate Racemase
KeywordsISOMERASE / Racemase
Function / homology
Function and homology information


glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
Glutamate racemase / Asp/Glu racemase, active site 2 / 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
Biological speciesStreptococcus pyogenes M1 GAS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKim, E.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural basis for glutamate racemase inhibition
Authors: Kim, K.H. / Bong, Y.J. / Park, J.K. / Shin, K.J. / Hwang, K.Y. / Kim, E.E.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)60,1624
Polymers59,9702
Non-polymers1922
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.397, 88.951, 95.107
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: 29985.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes M1 GAS (bacteria)
Species: Streptococcus pyogenes / Strain: ATCC 700294 / Gene: murI / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9A1B7, glutamate racemase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG4000, 10% Glycerol, 0.2M MgSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2005 / Details: wiggler
RadiationMonochromator: wiggler / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 27842 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 33.3
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 4.7 / % possible all: 80.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OHG

2ohg


Resolution: 2.25→40.29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 87226.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2652 9.9 %RANDOM
Rwork0.207 ---
obs0.207 26697 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.6627 Å2 / ksol: 0.364427 e/Å3
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å20 Å20 Å2
2--0.74 Å20 Å2
3----5.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.25→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4032 0 10 229 4271
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it3.431.5
X-RAY DIFFRACTIONc_mcangle_it5.572
X-RAY DIFFRACTIONc_scbond_it6.222
X-RAY DIFFRACTIONc_scangle_it9.562.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 401 9.7 %
Rwork0.25 3747 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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