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Yorodumi- PDB-2gra: crystal structure of Human Pyrroline-5-carboxylate Reductase comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gra | ||||||
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Title | crystal structure of Human Pyrroline-5-carboxylate Reductase complexed with nadp | ||||||
Components | Pyrroline-5-carboxylate reductase 1 | ||||||
Keywords | OXIDOREDUCTASE / Human Pyrroline-5-carboxylate Reductase / NADPH | ||||||
Function / homology | Function and homology information pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / proline biosynthetic process / L-proline biosynthetic process / Glutamate and glutamine metabolism / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / cellular response to oxidative stress / mitochondrial matrix / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Meng, Z. / Lou, Z. / Liu, Z. / Rao, Z. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal structure of human pyrroline-5-carboxylate reductase Authors: Meng, Z. / Lou, Z. / Liu, Z. / Li, M. / Zhao, X. / Bartlam, M. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gra.cif.gz | 285 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gra.ent.gz | 229.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/2gra ftp://data.pdbj.org/pub/pdb/validation_reports/gr/2gra | HTTPS FTP |
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-Related structure data
Related structure data | 2gerSC 2gr9C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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5 |
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7 |
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Unit cell |
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-Components
#1: Protein | Mass: 29147.648 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P32322, pyrroline-5-carboxylate reductase #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-GLU / #4: 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: 4.51 Å3/Da / Density % sol: 72.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.8-1M sodium acetate, 30-40mM imidazole (pH 6.5), 50-60mM Tris-HCl (pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 27, 2005 |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 535608 / Num. obs: 535337 / % possible obs: 99 % / Observed criterion σ(F): 0 |
Reflection shell | Resolution: 3.1→3.2 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GER Resolution: 3.1→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.1→50 Å
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Refine LS restraints |
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