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- PDB-4at0: The crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogen... -
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Open data
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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 | ||||||
![]() | 3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / DEHYDOGENASE / STEROID CATABOLISM | ||||||
Function / homology | ![]() steroid dehydrogenase activity, acting on the CH-CH group of donors / steroid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van Oosterwijk, N. / Knol, J. / Dijkhuizen, L. / van der Geize, R. / Dijkstra, B.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.5 KB | Display | ![]() |
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PDB format | ![]() | 161.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 748.1 KB | Display | ![]() |
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Full document | ![]() | 751.2 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4at2C ![]() 1d4cS ![]() 1e39S ![]() 1kf6S ![]() 1nekS ![]() 1zoyS C: citing same article ( S: Starting model for refinement |
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Similar 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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Components on special symmetry positions |
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Details | THE BIOLOGICAL UNIT IS UNDETERMINED BY THE AUTHOR |
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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 613 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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