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Yorodumi- PDB-3tri: Structure of a pyrroline-5-carboxylate reductase (proC) from Coxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tri | ||||||
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Title | Structure of a pyrroline-5-carboxylate reductase (proC) from Coxiella burnetii | ||||||
Components | Pyrroline-5-carboxylate reductase | ||||||
Keywords | OXIDOREDUCTASE / Amino acid biosynthesis | ||||||
Function / homology | Function and homology information pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Coxiella burnetii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.5 Å | ||||||
Authors | Cheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J. | ||||||
Citation | Journal: Proteins / Year: 2015 Title: Structural genomics for drug design against the pathogen Coxiella burnetii. Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tri.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tri.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 3tri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/3tri ftp://data.pdbj.org/pub/pdb/validation_reports/tr/3tri | HTTPS FTP |
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-Related structure data
Related structure data | 3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqiC 3tqjC 3tqlC 3tqmC 3tqnC 3tqoC 3tqpC 3tqqC 3tqrC 3tqsC 3tqtC 3tquC 3tqwC 3tqxC 3tqyC 3tqzC 3tr0C 3tr1C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C 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: 30762.244 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: CBU_2090, proC / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q83A21, pyrroline-5-carboxylate reductase #2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-CL / | #5: 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: 2.52 Å3/Da / Density % sol: 51.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 0.1M glycine, 1.2M sodium dihydrogen phosphate, 0.8M dipotassium hydrogen phosphate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 21008 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.087 / Χ2: 0.69 / Net I/σ(I): 7.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→37.705 Å / Occupancy max: 1 / Occupancy min: 0.54 / FOM work R set: 0.8301 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.27 Å2 / ksol: 0.389 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.64 Å2 / Biso mean: 42.5074 Å2 / Biso min: 17.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→37.705 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %
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