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Yorodumi- PDB-7zcj: Crystal structure of Pizza6-TNH-TSH with Silicotungstic Acid (STA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zcj | ||||||||||||
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Title | Crystal structure of Pizza6-TNH-TSH with Silicotungstic Acid (STA) polyoxometalate | ||||||||||||
Components | Pizza6-TNH-TSH | ||||||||||||
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 / molecular replacement / Resolution: 1.56 Å | ||||||||||||
Authors | Wouters, S.M.L. / Kamata, K. / Takahashi, K. / Vandebroek, L. / Parac-Vogt, T.N. / Tame, J.R.H. / Voet, A.R.D. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: To be published Title: Mutational study of a symmetry matched protein-polyoxometalate interface Authors: Wouters, S. / 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 | 7zcj.cif.gz | 115.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zcj.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zcj_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7zcj_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7zcj_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 7zcj_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/7zcj ftp://data.pdbj.org/pub/pdb/validation_reports/zc/7zcj | HTTPS FTP |
-Related structure data
Related structure data | 7zphC 7zpzC 7zq2C 7zqgC 3ww9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 25869.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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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: 3.05 Å3/Da / Density % sol: 59.67 % / Mosaicity: 0.08 ° |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 6.5 Details: 0.1 M Magnesium chloride, 0.1 M MES pH 6.5, 30% (w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.56→47.73 Å / Num. obs: 46485 / % possible obs: 100 % / Redundancy: 24.8 % / Biso Wilson estimate: 16.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.019 / Rrim(I) all: 0.096 / Net I/σ(I): 27.7 / Num. measured all: 1154947 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WW9 Resolution: 1.56→47.73 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.86 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.24 Å2 / Biso mean: 27.5227 Å2 / Biso min: 12.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.56→47.73 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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