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Open data
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Basic information
Entry | Database: PDB / ID: 6rug | ||||||
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Title | Co-substituted alpha-Keggin bound to Proteinase K solved by MR | ||||||
![]() | Proteinase K | ||||||
![]() | PROTEIN BINDING / Polyoxometalate / Complex / alpha-Keggin / Proteinase K | ||||||
Function / homology | ![]() peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Breibeck, J. / Bijelic, A. / Rompel, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Transition metal-substituted Keggin polyoxotungstates enabling covalent attachment to proteinase K upon co-crystallization. Authors: Breibeck, J. / Bijelic, A. / Rompel, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.2 KB | Display | ![]() |
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PDB format | ![]() | 132.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ruhC ![]() 6rukC ![]() 6runC ![]() 6ruwC ![]() 6rveC ![]() 6rvgC ![]() 1ic6S 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 on special symmetry positions |
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Components
#1: Protein | Mass: 28958.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM sodium acetate (pH 5.5), 0.7-1.2 M ammonium sulphate, 2.5 mM Co-substituted alpha-Keggin |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→35 Å / Num. obs: 184016 / % possible obs: 99.33 % / Redundancy: 4 % / CC1/2: 0.973 / Rmerge(I) obs: 0.1743 / Rpim(I) all: 0.09364 / Net I/σ(I): 5.04 |
Reflection shell | Resolution: 1.1→1.139 Å / Num. unique obs: 737740 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IC6 Resolution: 1.1→34.996 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 14.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→34.996 Å
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Refine LS restraints |
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LS refinement shell |
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