+Open data
-Basic information
Entry | Database: PDB / ID: 6rve | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Co-substituted beta-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 space / metal ion binding Similarity search - Function | |||||||||
Biological species | Parengyodontium album (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||
Authors | Breibeck, J. / Bijelic, A. / Rompel, A. | |||||||||
Funding support | Austria, 1items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6rve.cif.gz | 175.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rve.ent.gz | 140.3 KB | Display | PDB format |
PDBx/mmJSON format | 6rve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rve_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6rve_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6rve_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 6rve_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/6rve ftp://data.pdbj.org/pub/pdb/validation_reports/rv/6rve | HTTPS FTP |
-Related structure data
Related structure data | 6rugC 6ruhC 6rukC 6runC 6ruwC 6rvgC 1ic6S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#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 |
---|
-Non-polymers , 5 types, 394 molecules
#2: Chemical | ChemComp-XCO / |
---|---|
#3: Chemical | ChemComp-KCO / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-BET / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.94 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100 mM sodium acetate (pH 4.5), 0.3-0.7 M ammonium acetate, 0.5 M betaine, 10 mM Co-substituted beta-Keggin |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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: 1.15→35.83 Å / Num. obs: 169779 / % possible obs: 98.67 % / Redundancy: 3.9 % / CC1/2: 0.982 / Rmerge(I) obs: 0.1695 / Rpim(I) all: 0.09024 / Net I/σ(I): 3.63 |
Reflection shell | Resolution: 1.15→1.191 Å / Num. unique obs: 15345 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IC6 Resolution: 1.15→35.83 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 27.32
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→35.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|