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Yorodumi- PDB-1afs: RECOMBINANT RAT LIVER 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE (3-ALP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1afs | ||||||
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Title | RECOMBINANT RAT LIVER 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE (3-ALPHA-HSD) COMPLEXED WITH NADP AND TESTOSTERONE | ||||||
Components | 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / NAD | ||||||
Function / homology | Function and homology information Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Prednisone ADME / 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / androsterone dehydrogenase (B-specific) activity / Retinoid metabolism and transport / steroid dehydrogenase activity / androsterone dehydrogenase activity / ketosteroid monooxygenase activity ...Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Prednisone ADME / 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / androsterone dehydrogenase (B-specific) activity / Retinoid metabolism and transport / steroid dehydrogenase activity / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / progesterone metabolic process / daunorubicin metabolic process / doxorubicin metabolic process / bile acid binding / aldose reductase (NADPH) activity / prostaglandin metabolic process / steroid metabolic process / hippocampus development / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bennett, M.J. / Albert, R.H. / Jez, J.M. / Ma, H. / Penning, T.M. / Lewis, M. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Steroid recognition and regulation of hormone action: crystal structure of testosterone and NADP+ bound to 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase. Authors: Bennett, M.J. / Albert, R.H. / Jez, J.M. / Ma, H. / Penning, T.M. / Lewis, M. #1: Journal: Biochemistry / Year: 1996 Title: Structure of 3 Alpha-Hydroxysteroid/Dihydrodiol Dehydrogenase Complexed with Nadp+ Authors: Bennett, M.J. / Schlegel, B.P. / Jez, J.M. / Penning, T.M. / Lewis, M. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Three-Dimensional Structure of Rat Liver 3 Alpha-Hydroxysteroid/Dihydrodiol Dehydrogenase: A Member of the Aldo-Keto Reductase Superfamily Authors: Hoog, S.S. / Pawlowski, J.E. / Alzari, P.M. / 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 | 1afs.cif.gz | 137 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1afs.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 1afs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/1afs ftp://data.pdbj.org/pub/pdb/validation_reports/af/1afs | HTTPS FTP |
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-Related structure data
Related structure data | 1lwiS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.956096, -0.220739, -0.192756), Vector: |
-Components
#1: Protein | Mass: 37192.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Production host: unidentified (others) References: UniProt: P23457, 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) #2: Chemical | #3: Chemical | #4: 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: 2.49 Å3/Da / Density % sol: 50.66 % | ||||||||||||||||||||
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Crystal grow | pH: 6.4 / Details: pH 6.4 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: SUPPER DOUBLE MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 26156 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.5→2.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.3 / % possible all: 92.7 |
Reflection shell | *PLUS % possible obs: 92.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LWI Resolution: 2.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.7 Å / Total num. of bins used: 6 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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