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Open data
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Basic information
Entry | Database: PDB / ID: 8f65 | ||||||
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Title | Crystal structure of VACV D13 in complex with BBL030900 | ||||||
![]() | Scaffold protein D13 | ||||||
![]() | VIRAL PROTEIN / poxvirus / assembly / scaffolding protein / Fragment-based drug design / immature virion | ||||||
Function / homology | Poxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / FORMIC ACID / 8-methoxyquinolin-4-amine / Scaffold protein OPG125![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Subedi, B.P. / Garriga, D. / Coulibaly, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of scaffolidng protein D13 of Vaccinia Virus in complex with fragments inhibiting A17 binding. Authors: Subedi, B.P. / Garriga, D. / Coulibaly, F. #1: ![]() Title: Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin. Authors: Garriga, D. / Headey, S. / Accurso, C. / Gunzburg, M. / Scanlon, M. / Coulibaly, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 415.3 KB | Display | ![]() |
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PDB format | ![]() | 272.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 886.4 KB | Display | ![]() |
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Full document | ![]() | 900.6 KB | Display | |
Data in XML | ![]() | 59.3 KB | Display | |
Data in CIF | ![]() | 83.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f47C ![]() 6beiS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 65050.840 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P68440 #2: Chemical | ChemComp-FMT / #3: Chemical | ChemComp-QF6 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1.7 - 2.2 M sodium formate and 0.1 M citric acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→47.77 Å / Num. obs: 64478 / % possible obs: 100 % / Redundancy: 24.5 % / Biso Wilson estimate: 53.09 Å2 / CC1/2: 0.996 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2.85→2.92 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4476 / CC1/2: 0.873 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BEI Resolution: 2.85→46.26 Å / SU ML: 0.3617 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.914 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 48.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→46.26 Å
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Refine LS restraints |
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LS refinement shell |
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