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- PDB-8b8o: Crystal structure of Scribble PDZ1 with human papillomavirus stra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b8o | |||||||||
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Title | Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Stewart, B.Z. / Kvansakul, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide Authors: Stewart, B.Z. / Caria, S. / Humbert, P.O. / Kvansakul, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.7 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8b82C ![]() 8b87C ![]() 8b9tC ![]() 8biaC ![]() 8bj0C ![]() 6xa6S 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (0.964038778597, 0.123768590064, -0.23518199224), (0.0639915060671, -0.967003924289, -0.246593790595), (-0.257942475199, 0.222676326812, -0.940149420553)Vector: 4. ...NCS oper: (Code: given Matrix: (0.964038778597, 0.123768590064, -0.23518199224), Vector ![]() |
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Components
#1: Protein | Mass: 10082.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: At the n-terminal of chain A, B, the sequence GPLGS is part of the expression tag Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1080.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.16 % / Description: Diamond plate |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 0.1 M Na HEPES pH 7.9, 63% v/v MPD |
-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: Feb 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→32.03 Å / Num. obs: 4654 / % possible obs: 99.57 % / Redundancy: 7 % / Biso Wilson estimate: 84.26 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1438 / Net I/σ(I): 8.41 |
Reflection shell | Resolution: 2.9→3.004 Å / Rmerge(I) obs: 1.293 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 451 / CC1/2: 0.594 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6XA6 Resolution: 2.9→32.03 Å / SU ML: 0.5153 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5046 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.69 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→32.03 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 3.10947417099 Å | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 21.3400575757 Å / Origin y: -25.5439849334 Å / Origin z: 1.20771914627 Å
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Refinement TLS group | Selection details: all |