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- PDB-2ohg: Structural Basis for Glutamte Racemase Inhibition -

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Basic information

Entry
Database: PDB / ID: 2ohg
TitleStructural Basis for Glutamte Racemase Inhibition
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 / MAD / Resolution: 2.5 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 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate racemase


Theoretical massNumber of molelcules
Total (without water)29,0481
Polymers29,0481
Non-polymers00
Water1,910106
1
A: Glutamate racemase

A: Glutamate racemase


Theoretical massNumber of molelcules
Total (without water)58,0962
Polymers58,0962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)81.581, 81.581, 100.237
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glutamate racemase


Mass: 29048.033 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 8% PEG6000, 7% Glycerol, 0.1M Bicine, pH 8.6, 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: 0.97956, 0.97969, 0.97189
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2005 / Details: wiggler
RadiationMonochromator: wiggler / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979561
20.979691
30.971891
ReflectionResolution: 2.5→50 Å / Num. obs: 23929 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 28.6
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.04 / % possible all: 79.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→40.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 97868.09 / 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
Rfree0.264 1131 4.7 %RANDOM
Rwork0.209 ---
obs0.209 23929 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.4565 Å2 / ksol: 0.33089 e/Å3
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å22.38 Å20 Å2
2---0.9 Å20 Å2
3---1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 0 106 2137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it5.251.5
X-RAY DIFFRACTIONc_mcangle_it7.962
X-RAY DIFFRACTIONc_scbond_it8.122
X-RAY DIFFRACTIONc_scangle_it12.362.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 123 4 %
Rwork0.302 2988 -
obs--71.9 %
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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