+Open data
-Basic information
Entry | Database: PDB / ID: 1hxh | ||||||
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Title | COMAMONAS TESTOSTERONI 3BETA/17BETA HYDROXYSTEROID DEHYDROGENASE | ||||||
Components | 3BETA/17BETA-HYDROXYSTEROID DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta / Rossmann fold / short-chain dehydrogenase | ||||||
Function / homology | Function and homology information 3(or 17)beta-hydroxysteroid dehydrogenase / testosterone dehydrogenase [NAD(P)+] activity / dihydrotestosterone 17-beta-dehydrogenase activity / steroid metabolic process Similarity search - Function | ||||||
Biological species | Comamonas testosteroni (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Benach, J. / Filling, C. / Oppermann, U.C.T. / Roversi, P. / Bricogne, G. / Berndt, K.D. / Jornvall, H. / Ladenstein, R. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structure of Bacterial 3beta/17beta-Hydroxysteroid Dehydrogenase at 1.2 A Resolution: A Model for Multiple Steroid Recognition Authors: Benach, J. / Filling, C. / Oppermann, U.C.T. / Roversi, P. / Bricogne, G. / Berndt, K.D. / Jornvall, H. / Ladenstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hxh.cif.gz | 414 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hxh.ent.gz | 339.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hxh_validation.pdf.gz | 382.6 KB | Display | wwPDB validaton report |
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Full document | 1hxh_full_validation.pdf.gz | 397.3 KB | Display | |
Data in XML | 1hxh_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 1hxh_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/1hxh ftp://data.pdbj.org/pub/pdb/validation_reports/hx/1hxh | HTTPS FTP |
-Related structure data
Related structure data | 2hsdS 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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-Components
#1: Protein | Mass: 26847.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni (bacteria) / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 References: UniProt: P19871, 3(or 17)beta-hydroxysteroid dehydrogenase #2: 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: 2.36 Å3/Da / Density % sol: 47.58 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% Ethanol, 250 mM NaCl, 50 mM Tris/HCl, 10 mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8424 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8424 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→40 Å / Num. all: 1409412 / Num. obs: 1409412 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -1 / Redundancy: 4 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 1.22→1.25 Å / Rmerge(I) obs: 0.383 / % possible all: 83.9 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 314581 / Num. measured all: 1409412 |
Reflection shell | *PLUS % possible obs: 83.9 % / Mean I/σ(I) obs: 54.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HSD Resolution: 1.22→20 Å / SU ML: 0.15 / Cross valid method: free / σ(F): 0 / σ(I): 0 / ESU R: 0.16 / ESU R Free: 0.17
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Displacement parameters | Biso mean: 19 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→20 Å / Rfactor Rfree: 0.18 / Rfactor Rwork: 0.146 | |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.18 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.172 / Rfactor Rwork: 0.139 |