+Open data
-Basic information
Entry | Database: PDB / ID: 2oho | ||||||
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Title | Structural Basis for Glutamate Racemase Inhibitor | ||||||
Components | Glutamate Racemase | ||||||
Keywords | ISOMERASE / 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 | ||||||
Biological species | Streptococcus pyogenes M1 GAS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Kim, E.E. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oho.cif.gz | 116.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oho.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 2oho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/2oho ftp://data.pdbj.org/pub/pdb/validation_reports/oh/2oho | HTTPS FTP |
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-Related structure data
Related structure data | 2ohgSC 2ohvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.44 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2005 / Details: wiggler |
Radiation | Monochromator: wiggler / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 4.7 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.6627 Å2 / ksol: 0.364427 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→40.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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