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Yorodumi- PDB-3bhj: Crystal structure of human Carbonyl Reductase 1 in complex with g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bhj | ||||||
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Title | Crystal structure of human Carbonyl Reductase 1 in complex with glutathione | ||||||
Components | Carbonyl reductase [NADPH] 1 | ||||||
Keywords | OXIDOREDUCTASE / NADP | ||||||
Function / homology | Function and homology information 15-hydroxyprostaglandin-D dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) / alcohol dehydrogenase [NAD(P)+] / 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+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) / alcohol dehydrogenase [NAD(P)+] / 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 (NADP+) activity / 15-hydroxyprostaglandin-D 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: 1.77 Å | ||||||
Authors | Rauh, D. / Bateman, R.L. / 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 | 3bhj.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bhj.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bhj_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 3bhj_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 3bhj_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 3bhj_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/3bhj ftp://data.pdbj.org/pub/pdb/validation_reports/bh/3bhj | HTTPS FTP |
-Related structure data
Related structure data | 3bhiC 3bhmC 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 , 7 types, 279 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-NAP / | #5: Chemical | ChemComp-GSH / | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: 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: 2.4 Å3/Da / Density % sol: 48.66 % |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→27 Å / Num. obs: 27157 / % possible obs: 93.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.029 / Χ2: 1.035 / Net I/σ(I): 32.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.77→26.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.757 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.113 / 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: 15.277 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→26.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.816 Å / Total num. of bins used: 20
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