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Yorodumi- PDB-8p2u: Crystal structure of S6BE with Silicotungstic Acid (STA) polyoxom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p2u | ||||||||||||
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Title | Crystal structure of S6BE with Silicotungstic Acid (STA) polyoxometalate | ||||||||||||
Components | S6BE | ||||||||||||
Keywords | UNKNOWN FUNCTION / beta propeller / synthetic / designer / polyoxometalate / STA / co-crystal / silicotungstic acid | ||||||||||||
Function / homology | Keggin (STA) Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||||||||
Authors | Wouters, S.M.L. / Kamata, K. / Vandebroek, L. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: To be published Title: Crystal structure of S6BE with Silicotungstic Acid (STA) polyoxometalate Authors: Wouters, S.M.L. / Kamata, K. / Takahashi, K. / Vandebroek, L. / Parac-Vogt, T.N. / Tame, J.R.H. / 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 | 8p2u.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p2u.ent.gz | 129.7 KB | Display | PDB format |
PDBx/mmJSON format | 8p2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p2u_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8p2u_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8p2u_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 8p2u_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/8p2u ftp://data.pdbj.org/pub/pdb/validation_reports/p2/8p2u | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30458.453 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 | ChemComp-SIW / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.43 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 5 / Details: 1.5 M Sodium malonate, pH 5.0 |
-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 EIGER X 16M / Detector: PIXEL / Date: Apr 23, 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: 1.4→38.38 Å / Num. obs: 61953 / % possible obs: 94.9 % / Redundancy: 1.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.06 / Rrim(I) all: 0.084 / Χ2: 0.96 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.4→1.42 Å / % possible obs: 93.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.134 / Num. measured all: 3386 / Num. unique obs: 1866 / CC1/2: 0.944 / Rpim(I) all: 0.134 / Rrim(I) all: 0.189 / Χ2: 0.41 / Net I/σ(I) obs: 5.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.38 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2.08 / Phase error: 21.67 / 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: 1.4→38.38 Å
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Refine LS restraints |
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LS refinement shell |
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