+Open data
-Basic information
Entry | Database: PDB / ID: 8f65 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of VACV D13 in complex with BBL030900 | ||||||
Components | Scaffold protein D13 | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Subedi, B.P. / Garriga, D. / Coulibaly, F. | ||||||
Funding support | Australia, 1items
| ||||||
Citation | Journal: To Be Published 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: Journal: Proc Natl Acad Sci U S A / Year: 2018 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8f65.cif.gz | 415.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8f65.ent.gz | 272.1 KB | Display | PDB format |
PDBx/mmJSON format | 8f65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f65_validation.pdf.gz | 886.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8f65_full_validation.pdf.gz | 900.6 KB | Display | |
Data in XML | 8f65_validation.xml.gz | 59.3 KB | Display | |
Data in CIF | 8f65_validation.cif.gz | 83.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/8f65 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/8f65 | HTTPS FTP |
-Related structure data
Related structure data | 8f47C 6beiS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 65050.840 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: VACWR118, D13L Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P68440 #2: Chemical | ChemComp-FMT / #3: Chemical | ChemComp-QF6 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.24 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|