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- PDB-1fjh: THE CRYSTAL STRUCTURE OF 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE FRO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fjh | ||||||
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Title | THE CRYSTAL STRUCTURE OF 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE FROM COMAMONAS TESTOSTERONI, A MEMBER OF THE SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY | ||||||
![]() | 3ALPHA-HYDROXYSTEROID DEHYDROGENASE/CARBONYL REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / Short Chain Dehydrogenase / SDR / Carbonyl Reductase / Steroid / Hydroxysteroid / Xenobiotic / Metyrapone / Oligomerisation / Comamonas testosteroni | ||||||
Function / homology | ![]() 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) / androsterone dehydrogenase (B-specific) activity / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Grimm, C. / Ficner, R. / Maser, E. / Klebe, G. / Reuter, K. | ||||||
![]() | ![]() Title: The crystal structure of 3alpha -hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni shows a novel oligomerization pattern within the short chain dehydrogenase/reductase family. Authors: Grimm, C. / Maser, E. / Mobus, E. / Klebe, G. / Reuter, K. / Ficner, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105 KB | Display | ![]() |
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PDB format | ![]() | 79.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 374 KB | Display | ![]() |
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Full document | ![]() | 381.4 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly is a dimer constructed from chain A by the two-fold NCS axis. |
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Components
#1: Protein | Mass: 26420.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q9ZFY9, UniProt: P80702*PLUS, 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.96 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG4000, ammonium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 7.5 / Details: used macroseeding | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30.02 Å / Num. all: 50140 / Num. obs: 50140 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.46 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 69.7 |
Reflection shell | Resolution: 1.65→1.66 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.271 / % possible all: 74 |
Reflection | *PLUS Num. measured all: 374072 |
Reflection shell | *PLUS % possible obs: 74 % |
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Processing
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Refinement | Resolution: 1.68→30.02 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 548597.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.62 Å2 / ksol: 0.339 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.68→30.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.79 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.289 / % reflection Rfree: 3.9 % / Rfactor Rwork: 0.256 |