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Yorodumi- PDB-2hrb: Crystal Structure of human Carbonyl Reductase 3, complexed with NADP+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hrb | ||||||
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Title | Crystal Structure of human Carbonyl Reductase 3, complexed with NADP+ | ||||||
Components | Carbonyl reductase [NADPH] 3 | ||||||
Keywords | OXIDOREDUCTASE / Retinol / dehydrogenase / peroxisome / structural genomics / short-chain dehydrogenase/reductase / structural genomics consortium / SGC | ||||||
Function / homology | Function and homology information phylloquinone catabolic process / 3-keto sterol reductase activity / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / Phase I - Functionalization of compounds / NADPH binding / xenobiotic metabolic process / cognition / extracellular space / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Pilka, E.S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of human Carbonyl Reductase 3, complexed with NADP+ Authors: Pilka, E.S. / Rojkova, A. / Kavanagh, K.L. / Niesen, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hrb.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hrb.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 2hrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/2hrb ftp://data.pdbj.org/pub/pdb/validation_reports/hr/2hrb | HTTPS FTP |
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-Related structure data
Related structure data | 1wmaS S: Starting model for refinement |
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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: 30538.818 Da / Num. of mol.: 1 / Fragment: residues 4-277 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-SGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-R3 / References: UniProt: O75828, carbonyl reductase (NADPH) | ||
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#2: Chemical | ChemComp-NAP / | ||
#3: Chemical | #4: 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: 2.43 Å3/Da / Density % sol: 49.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8M tri-ammonium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 19, 2006 / Details: OSMIC |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.673 Å / Num. all: 24260 / Num. obs: 24038 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3 / Num. unique all: 3417 / Rsym value: 0.391 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WMA Resolution: 1.9→30.06 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.976 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.156 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: 11.539 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.0805 Å / Origin y: 12.5816 Å / Origin z: 13.5933 Å
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