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Yorodumi- PDB-3fjn: The crystal structure of 17-alpha hydroxysteroid dehydrogenase Y2... -
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-Basic information
Entry | Database: PDB / ID: 3fjn | ||||||
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Title | The crystal structure of 17-alpha hydroxysteroid dehydrogenase Y224D mutant. | ||||||
Components | Aldo-keto reductase family 1 member C21 | ||||||
Keywords | OXIDOREDUCTASE / Aldo-keto reductase / 17-alpha-hydroxysteroid dehydrogenase / Cytoplasm / Lipid metabolism / NADP / Phosphoprotein / Steroid metabolism | ||||||
Function / homology | Function and homology information 17-beta-ketosteroid reductase activity / chlordecone reductase activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / androsterone dehydrogenase (B-specific) activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / steroid dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / phenanthrene 9,10-monooxygenase activity ...17-beta-ketosteroid reductase activity / chlordecone reductase activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / androsterone dehydrogenase (B-specific) activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / steroid dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / carboxylic acid binding / 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 / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / retinal dehydrogenase activity / bile acid binding / aldose reductase (NADPH) activity / NADP+ binding / steroid metabolic process / NADPH binding / steroid binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Dhagat, U. / El-Kabbani, O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Studies on a Tyr residue critical for the binding of coenzyme and substrate in mouse 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21): structure of the Y224D mutant enzyme 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 | 3fjn.cif.gz | 148.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fjn.ent.gz | 116.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/3fjn ftp://data.pdbj.org/pub/pdb/validation_reports/fj/3fjn | HTTPS FTP |
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-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: CYS / Beg label comp-ID: CYS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth seq-ID: 7 - 323 / Label seq-ID: 7 - 323
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-Components
#1: Protein | Mass: 36876.492 Da / Num. of mol.: 2 / Mutation: Y224D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pkk223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q91WR5, 3(or 17)alpha-hydroxysteroid dehydrogenase #2: Chemical | ChemComp-ACT / #3: 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: 2.2 Å3/Da / Density % sol: 44.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Sodium Cacodylate, 0.2M Magnesium Acetate, 20% Polyethylene glycol8000, pH 6.5, 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: Sep 4, 2008 / 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: 2.3→30 Å / Num. obs: 28098 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.34 % / Rmerge(I) obs: 0.0552 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.24 % / Rmerge(I) obs: 0.1343 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2085 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2P5N Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.887 / SU B: 7.443 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.422 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. SOME OF WATERS LISTED IN REMARK 525 ARE FITTED CLOSE TO THE GENERATED SYMMETRY ATOMS OF THE PROTEIN.
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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: 28.888 Å2
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Refine analyze | Luzzati coordinate error obs: 0.275 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→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: 2471 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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