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Yorodumi- PDB-1ihi: Crystal Structure of Human Type III 3-alpha-Hydroxysteroid Dehydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ihi | ||||||
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Title | Crystal Structure of Human Type III 3-alpha-Hydroxysteroid Dehydrogenase/Bile Acid Binding Protein (AKR1C2) Complexed with NADP+ and Ursodeoxycholate | ||||||
Components | 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / ALPHA-BETA BARREL / TERNARY COMPLEX / PROTEIN-NADP-BILE ACID COMPLEX | ||||||
Function / homology | Function and homology information indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / : / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase ...indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / : / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / cellular response to prostaglandin D stimulus / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / carboxylic acid binding / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / Oxidoreductases / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / bile acid binding / aldose reductase (NADPH) activity / prostaglandin metabolic process / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / digestion / epithelial cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Jin, Y. / Stayrook, S.E. / Albert, R.H. / Palackal, N.T. / Penning, T.M. / Lewis, M. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal structure of human type III 3alpha-hydroxysteroid dehydrogenase/bile acid binding protein complexed with NADP(+) and ursodeoxycholate. Authors: Jin, Y. / Stayrook, S.E. / Albert, R.H. / Palackal, N.T. / Penning, T.M. / Lewis, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ihi.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ihi.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ihi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ihi_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1ihi_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1ihi_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 1ihi_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ihi ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ihi | HTTPS FTP |
-Related structure data
Related structure data | 1afsS 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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-Components
#1: Protein | Mass: 36786.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P52895, EC: 1.1.1.52 #2: Chemical | #3: Chemical | |
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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: 2.75 Å3/Da / Density % sol: 55.3 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 5000 MME, SODIUM CACODYLATE, AMMONIUM SULFATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 1998 / Details: MIRRORS |
Radiation | Monochromator: Charles Supper Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 16424 / Num. obs: 16424 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 50.48 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 6 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 12 / Num. unique all: 2219 / % possible all: 95.9 |
Reflection | *PLUS Num. measured all: 99026 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AFS.PDB Resolution: 3→8 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 15.7 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.18 Å / Rfactor Rfree error: 0.025
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 8 Å / σ(F): 3 / Rfactor obs: 0.223 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.7 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.376 / Rfactor Rwork: 0.289 |