+Open data
-Basic information
Entry | Database: PDB / ID: 2ohg | ||||||
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Title | Structural Basis for Glutamte Racemase Inhibition | ||||||
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 / MAD / Resolution: 2.5 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 | 2ohg.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ohg.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ohg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/2ohg ftp://data.pdbj.org/pub/pdb/validation_reports/oh/2ohg | HTTPS FTP |
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-Related 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: 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.87 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97956, 0.97969, 0.97189 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2005 / Details: wiggler | ||||||||||||
Radiation | Monochromator: wiggler / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 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 shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.04 / % possible all: 79.2 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.4565 Å2 / ksol: 0.33089 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→40.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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