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Yorodumi- PDB-6qsh: Crystal structure of the hybrid bioinorganic complex of Pizza6S l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qsh | |||||||||||||||
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Title | Crystal structure of the hybrid bioinorganic complex of Pizza6S linked by the 1:2 Ce-substituted Keggin | |||||||||||||||
Components | Pizza6S | |||||||||||||||
Keywords | DE NOVO PROTEIN / Artificial beta-propeller protein / computational design / polyoxometalate / POM / Pizza / polyoxometalate-protein framework / POM-protein framework / 1:2 Ce-substituted Keggin | |||||||||||||||
Function / homology | 1:2 Ce-substituted Keggin Function and homology information | |||||||||||||||
Biological species | Synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||||||||
Authors | Noguchi, H. / Vandebroek, L. / Kamata, K. / Tame, J.R.H. / Van Meervelt, L. / Parac-Vogt, T.N. / Voet, A.R.D. | |||||||||||||||
Funding support | Belgium, Japan, 4items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2020 Title: Hybrid assemblies of a symmetric designer protein and polyoxometalates with matching symmetry. Authors: Vandebroek, L. / Noguchi, H. / Kamata, K. / Tame, J.R.H. / Van Meervelt, L. / Parac-Vogt, T.N. / Voet, A.R.D. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qsh.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qsh.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 6qsh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qsh_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 6qsh_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6qsh_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 6qsh_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/6qsh ftp://data.pdbj.org/pub/pdb/validation_reports/qs/6qsh | HTTPS FTP |
-Related structure data
Related structure data | 6qsdC 6qseC 6qsfC 6qsgC 3ww9S S: Starting model for refinement C: citing same article (ref.) |
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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: 25719.295 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synthetic construct (others) / Production host: Escherichia coli (E. coli) | ||
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#2: Chemical | #3: 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: 2.43 Å3/Da / Density % sol: 49.41 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.05M Magnesium acetate, 0.1M Sodium acetate, 10% (w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.39 Å / Num. obs: 9133 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 6 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.146 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.5→2.6 Å / CC1/2: 0.802 / Rpim(I) all: 0.523 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ww9 Resolution: 2.5→42.368 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→42.368 Å
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Refine LS restraints |
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LS refinement shell |
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