+Open data
-Basic information
Entry | Database: PDB / ID: 6ruk | ||||||
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Title | Cu-substituted alpha-Keggin bound to Proteinase K solved by MR | ||||||
Components | Proteinase K | ||||||
Keywords | PROTEIN BINDING / Polyoxometalate / Complex / alpha-Keggin / Proteinase K | ||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Parengyodontium album (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Breibeck, J. / Bijelic, A. / Rompel, A. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ruk.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ruk.ent.gz | 104.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ruk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/6ruk ftp://data.pdbj.org/pub/pdb/validation_reports/ru/6ruk | HTTPS FTP |
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-Related structure data
Related structure data | 6rugC 6ruhC 6runC 6ruwC 6rveC 6rvgC 1ic6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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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-Components
#1: Protein | Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K |
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#2: Chemical | ChemComp-XCU / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.55 % |
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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, 5 mM Cu-substituted alpha-Keggin |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å |
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: 1.2→34.99 Å / Num. obs: 142531 / % possible obs: 99.79 % / Redundancy: 4.4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.1241 / Rpim(I) all: 0.06592 / Net I/σ(I): 8.35 |
Reflection shell | Resolution: 1.2→1.243 Å / Num. unique obs: 14209 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ic6 Resolution: 1.2→34.99 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 14.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→34.99 Å
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Refine LS restraints |
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LS refinement shell |
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