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Yorodumi- PDB-3bhm: Crystal structure of human Carbonyl Reductase 1 in complex with S... -
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-Basic information
Entry | Database: PDB / ID: 3bhm | ||||||
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Title | Crystal structure of human Carbonyl Reductase 1 in complex with S-hydroxymethylglutathione | ||||||
Components | Carbonyl reductase [NADPH] 1 | ||||||
Keywords | OXIDOREDUCTASE / Acetylation / Cytoplasm / NADP / Polymorphism | ||||||
Function / homology | Function and homology information alcohol dehydrogenase [NAD(P)+] / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) activity / prostaglandin-E2 9-reductase / prostaglandin E2 9-reductase activity / S-nitrosoglutathione reductase (NADPH) activity / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / vitamin K metabolic process ...alcohol dehydrogenase [NAD(P)+] / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) activity / prostaglandin-E2 9-reductase / prostaglandin E2 9-reductase activity / S-nitrosoglutathione reductase (NADPH) activity / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / vitamin K metabolic process / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / alcohol dehydrogenase (NADP+) activity / glucocorticoid metabolic process / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / epithelial cell differentiation / xenobiotic metabolic process / positive regulation of reactive oxygen species metabolic process / extracellular vesicle / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Bateman, R.L. / Rauh, D. / Shokat, K.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Human carbonyl reductase 1 is an s-nitrosoglutathione reductase Authors: Bateman, R.L. / Rauh, D. / Tavshanjian, B. / Shokat, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bhm.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bhm.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/3bhm ftp://data.pdbj.org/pub/pdb/validation_reports/bh/3bhm | HTTPS FTP |
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-Related structure data
Related structure data | 3bhiC 3bhjC 1wmaS S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30284.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBR1, CBR, CRN / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P16152, carbonyl reductase (NADPH) |
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-Non-polymers , 5 types, 207 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-AHE / | #4: Chemical | #5: Chemical | ChemComp-NAP / | #6: 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: 2.43 Å3/Da / Density % sol: 49.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: vapor diffusion, hanging drop, temperature 298K, pH7.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 24, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.66→50 Å / Num. obs: 34423 / % possible obs: 97.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.049 / Χ2: 0.848 / Net I/σ(I): 10.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WMA Resolution: 1.8→48.22 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.958 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.114 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.469 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.804→1.851 Å / Total num. of bins used: 20
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