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Yorodumi- PDB-1yqg: Crystal structure of a pyrroline-5-carboxylate reductase from nei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yqg | |||||||||
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Title | Crystal structure of a pyrroline-5-carboxylate reductase from neisseria meningitides mc58 | |||||||||
Components | pyrroline-5-carboxylate reductase | |||||||||
Keywords | OXIDOREDUCTASE / PYRROLINE-5-CARBOXYLATE REDUCTASE / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | |||||||||
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 | Neisseria meningitidis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | |||||||||
Authors | Chang, C. / Joachimiak, A. / Li, H. / Collart, F. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structures of Delta(1)-Pyrroline-5-carboxylate Reductase from Human Pathogens Neisseria meningitides and Streptococcus pyogenes Authors: Nocek, B. / Chang, C. / Li, H. / Lezondra, L. / Holzle, D. / Collart, F. / Joachimiak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yqg.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yqg.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/1yqg ftp://data.pdbj.org/pub/pdb/validation_reports/yq/1yqg | HTTPS FTP |
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-Related structure data
Related structure data | 2ag8C 2ahrC 2amfC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The second part of the biological assembly is generated by operation of 1-x, 1-y, Z |
-Components
#1: Protein | Mass: 28799.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K1N1 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.6 Å3/Da / Density % sol: 51.9 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: AMMONIUM SULFATE, HEPES, PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97984, 0.97970 | |||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 23, 2004 | |||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.61→50 Å / Num. all: 38574 / Num. obs: 26616 / % possible obs: 69 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 24.66 | |||||||||
Reflection shell | Resolution: 1.61→1.67 Å / % possible all: 0.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.742 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.446 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 29.29 Å / Origin y: 31.383 Å / Origin z: 15.071 Å
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Refinement TLS group |
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