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Yorodumi- PDB-4at0: The crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4at0 | ||||||
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Title | The crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogenase from Rhodococcus jostii RHA1 | ||||||
Components | 3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / DEHYDOGENASE / STEROID CATABOLISM | ||||||
Function / homology | Function and homology information steroid dehydrogenase activity, acting on the CH-CH group of donors / steroid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | RHODOCOCCUS JOSTII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | van Oosterwijk, N. / Knol, J. / Dijkhuizen, L. / van der Geize, R. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structure and Catalytic Mechanism of 3-Ketosteroid-{Delta}4-(5Alpha)-Dehydrogenase from Rhodococcus Jostii Rha1 Genome. Authors: Van Oosterwijk, N. / Knol, J. / Dijkhuizen, L. / Van Der Geize, R. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4at0.cif.gz | 204.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4at0.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 4at0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4at0_validation.pdf.gz | 748.1 KB | Display | wwPDB validaton report |
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Full document | 4at0_full_validation.pdf.gz | 751.2 KB | Display | |
Data in XML | 4at0_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 4at0_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/4at0 ftp://data.pdbj.org/pub/pdb/validation_reports/at/4at0 | HTTPS FTP |
-Related structure data
Related structure data | 4at2C 1d4cS 1e39S 1kf6S 1nekS 1zoyS C: citing same article (ref.) 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 on special symmetry positions |
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Details | THE BIOLOGICAL UNIT IS UNDETERMINED BY THE AUTHOR |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54083.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOCOCCUS JOSTII (bacteria) / Strain: RHA1 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0S4Q9, EC: 1.3.99.5 |
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-Non-polymers , 5 types, 613 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-FAD / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | TWO POINT MUTATIONS, COMPARED TO THE DATABASE SEQUENCE, WERE FOUND IN THE STRUCTURE. A60T AND ...TWO POINT MUTATIONS, COMPARED TO THE DATABASE SEQUENCE, WERE FOUND IN THE STRUCTURE. A60T AND T160A, AND CONFIRMED BY SEQUENCING |
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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: 3.06 Å3/Da / Density % sol: 59.8 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: CRYSTALS WERE OBTAINED FROM 200 MM AMMONIUM ACETATE, 100 MM SODIUM CITRATE PH 5.6 AND 30%(W/V) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 18, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→49.6 Å / Num. obs: 80282 / % possible obs: 97 % / Redundancy: 11.1 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.7 / % possible all: 83.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY Resolution: 1.6→39.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.117 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 16.802 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→39.65 Å
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Refine LS restraints |
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