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- PDB-6u4i: Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6u4i | ||||||
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Title | Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to Equilenin at 280 K | ||||||
![]() | Steroid Delta-isomerase![]() | ||||||
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Function / homology | Ketosteroid 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 | ![]() | 177 KB | Display | ![]() |
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PDB format | ![]() | 143.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tzdC ![]() 6u1zC ![]() 6ubqC ![]() 6ucnC ![]() 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 | 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: 2.23 Å3/Da / Density % sol: 44.73 % |
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Crystal grow![]() | Temperature: 298 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![]() | ||||||||||||||||||||||||
Reflection | Resolution: 1.55→36.831 Å / Num. obs: 37064 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 17.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.04 / Rrim(I) all: 0.085 / Net I/σ(I): 11.8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3VSY Resolution: 1.55→36.831 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.02 Å2 / Biso mean: 26.9062 Å2 / Biso min: 8.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→36.831 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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