+Open data
-Basic information
Entry | Database: PDB / ID: 1epv | ||||||
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Title | ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM D-CYCLOSERINE | ||||||
Components | ALANINE RACEMASE | ||||||
Keywords | ISOMERASE / alpha-beta barrel | ||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Fenn, T.D. / Stamper, G.F. / Morollo, A.A. / Ringe, D. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: A side reaction of alanine racemase: transamination of cycloserine. Authors: Fenn, T.D. / Stamper, G.F. / Morollo, A.A. / Ringe, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1epv.cif.gz | 163.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1epv.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 1epv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/1epv ftp://data.pdbj.org/pub/pdb/validation_reports/ep/1epv | 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: 43563.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: PMALR3 / Production host: Escherichia coli (E. coli) / References: UniProt: P10724, alanine 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: 2.19 Å3/Da / Density % sol: 43.78 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, sodium acetate, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→28.79 Å / Num. all: 39472 / Num. obs: 35816 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.339 / % possible all: 92.3 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 39472 / Num. measured all: 218570 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 92.3 % |
-Processing
Software |
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Refinement | Resolution: 2.2→28.79 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 259525.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.99 Å2 / ksol: 0.307 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→28.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. reflection obs: 31194 / Num. reflection Rfree: 2340 / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.208 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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