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Yorodumi- PDB-3cv6: The crystal structure of mouse 17-alpha hydroxysteroid dehydrogen... -
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-Basic information
Entry | Database: PDB / ID: 3cv6 | ||||||
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Title | The crystal structure of mouse 17-alpha hydroxysteroid dehydrogenase GG225.226PP mutant in complex with inhibitor and cofactor NADP+. | ||||||
Components | Aldo-keto reductase family 1 member C21 | ||||||
Keywords | OXIDOREDUCTASE / Aldo-keto reductase / Hydroxysteroid Dehydrogenase / Ternary Complex / Hexestrol / Lipid metabolism / NADP / Phosphoprotein / Steroid metabolism | ||||||
Function / homology | Function and homology information Synthesis of bile acids and bile salts via 24-hydroxycholesterol / 17-beta-ketosteroid reductase (NADPH) activity / RA biosynthesis pathway / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / Retinoid metabolism and transport / 3(or 17)alpha-hydroxysteroid dehydrogenase / steroid dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol ...Synthesis of bile acids and bile salts via 24-hydroxycholesterol / 17-beta-ketosteroid reductase (NADPH) activity / RA biosynthesis pathway / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / Retinoid metabolism and transport / 3(or 17)alpha-hydroxysteroid dehydrogenase / steroid dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Prednisone ADME / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / aldo-keto reductase (NADPH) activity / lithocholic acid binding / steroid biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / NADP+ binding / aldose reductase (NADPH) activity / steroid metabolic process / NADPH binding / steroid binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Dhagat, U. / El-Kabbani, O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structure of the G225P/G226P mutant of mouse 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21) ternary complex: implications for the binding of inhibitor and substrate. Authors: Dhagat, U. / Endo, S. / Mamiya, H. / Hara, A. / El-Kabbani, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cv6.cif.gz | 162.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cv6.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cv6_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3cv6_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3cv6_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 3cv6_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/3cv6 ftp://data.pdbj.org/pub/pdb/validation_reports/cv/3cv6 | HTTPS FTP |
-Related structure data
Related structure data | 2p5nS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth seq-ID: 1 - 323 / Label seq-ID: 1 - 323
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-Components
#1: Protein | Mass: 37004.707 Da / Num. of mol.: 2 / Mutation: G225P, G226P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Akr1c21 / Plasmid: pkk223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q91WR5, 3(or 17)alpha-hydroxysteroid dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-BME / #5: Water | ChemComp-HOH / | Sequence details | THERE ARE DIFFERENCES BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THIS IS A VARIANT AT THESE ...THERE ARE DIFFERENCE | |
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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: 2.94 Å3/Da / Density % sol: 58.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes, 10% PEG l6000, 5% 2-methyl-2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 17, 2007 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 46728 / Num. obs: 46635 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.01 % / Rmerge(I) obs: 0.0392 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.44 % / Rmerge(I) obs: 0.3672 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2p5n Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.418 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.221 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 36.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2619 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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