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- PDB-6ucn: Multi-conformer model of Ketosteroid Isomerase from Pseudomonas P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ucn | ||||||
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Title | Multi-conformer model of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to Equilenin at 250 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 / EQUILENIN / Steroid Delta-isomerase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yabukarski, F. / Herschlag, D. / Biel, J.T. / Fraser, J.S. | ||||||
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 | ![]() | 227.9 KB | Display | ![]() |
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PDB format | ![]() | 199.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.2 KB | Display | ![]() |
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Full document | ![]() | 497.1 KB | Display | |
Data in XML | ![]() | 1.5 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tzdC ![]() 6u1zC ![]() 6u4iC ![]() 6ubqC ![]() 6ucwC ![]() 6ucyC ![]() 3vsyS 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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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 | #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: 2.24 Å3/Da / Density % sol: 45.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.2 / Details: 17-23% PEG 3350, 0.2 M MAGNESIUM CHLORIDE / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 250 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: 0.88557 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.32→35.91 Å / Num. obs: 58753 / % possible obs: 97.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 13.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.033 / Rrim(I) all: 0.074 / Net I/σ(I): 12.4 / Num. measured all: 286924 / Scaling rejects: 80 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VSY Resolution: 1.32→32.2914 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.96 Å2 / Biso mean: 19.4081 Å2 / Biso min: 5.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.32→32.2914 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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