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- PDB-7zpz: Crystal structure of Pizza6-TSR-TSH with Silicotungstic Acid (STA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zpz | ||||||||||||
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Title | Crystal structure of Pizza6-TSR-TSH with Silicotungstic Acid (STA) polyoxometalate | ||||||||||||
![]() | Pizza6-TSR-TSH | ||||||||||||
![]() | UNKNOWN FUNCTION / beta propeller / synthetic / designer / polyoxometalate / STA / co-crystal / silicotungstic acid | ||||||||||||
Function / homology | Keggin (STA)![]() | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Wouters, S.M.L. / Kamata, K. / Takahashi, K. / Vandebroek, L. / Parac-Vogt, T.N. / Tame, J.R.H. / Voet, A.R.D. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.1 KB | Display | ![]() |
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PDB format | ![]() | 84.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zcjC ![]() 7zphC ![]() 7zq2C ![]() 7zqgC ![]() 3ww9S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 25845.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28a(+) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-SIW / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.03 % / Mosaicity: 0.09 ° |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion Details: 0.0085 M Cobalt chloride, 0.085 M MES pH 6.5, 1.53 M Ammonium sulfate, 15% (v/v) Glycerol PH range: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.57→42.77 Å / Num. obs: 30288 / % possible obs: 100 % / Redundancy: 25.9 % / Biso Wilson estimate: 16.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.035 / Rrim(I) all: 0.181 / Net I/σ(I): 16.5 / Num. measured all: 784827 / Scaling rejects: 640 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WW9 Resolution: 1.57→42.76 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.52 / 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: 53.72 Å2 / Biso mean: 20.6314 Å2 / Biso min: 8.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.57→42.76 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % 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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