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- PDB-6tzd: Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tzd | ||||||
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Title | Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to 4-Androstenedione at 280 K | ||||||
![]() | Steroid Delta-isomerase | ||||||
![]() | ISOMERASE | ||||||
Function / homology | Ketosteroid isomerase / steroid Delta-isomerase / SnoaL-like domain / SnoaL-like domain / steroid delta-isomerase activity / steroid metabolic process / NTF2-like domain superfamily / 4-ANDROSTENE-3-17-DIONE / Steroid Delta-isomerase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yabukarski, F. / Herschlag, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles. Authors: Yabukarski, F. / Biel, J.T. / Pinney, M.M. / Doukov, T. / Powers, A.S. / Fraser, J.S. / Herschlag, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.1 KB | Display | ![]() |
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PDB format | ![]() | 146.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.8 KB | Display | ![]() |
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Full document | ![]() | 364.8 KB | Display | |
Data in XML | ![]() | 1.4 KB | Display | |
Data in CIF | ![]() | 4.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u1zC ![]() 6u4iC ![]() 6ubqC ![]() 6ucnC ![]() 6ucwC ![]() 6ucyC ![]() 3vsyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14548.501 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 17-23 % PEG 3350, 0.2 M MAGNESIUM CHLORIDE / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 280 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→37.19 Å / Num. obs: 46456 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 19.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.023 / Rrim(I) all: 0.054 / Net I/σ(I): 18 / Num. measured all: 256187 / Scaling rejects: 35 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VSY Resolution: 1.4507→34.6595 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.99 Å2 / Biso mean: 33.3043 Å2 / Biso min: 10.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4507→34.6595 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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