+Open data
-Basic information
Entry | Database: PDB / ID: 3saq | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of D13, the scaffolding protein of vaccinia virus | ||||||
Components | Rifampicin resistance protein | ||||||
Keywords | VIRAL PROTEIN / double-barrel / jelly-roll / Scaffolding protein / structural protein / rifampicin-resistance protein / Surface of the immature virions and crescents | ||||||
Function / homology | Poxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / Scaffold protein OPG125 Function and homology information | ||||||
Biological species | Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å | ||||||
Authors | Coulibaly, F. | ||||||
Citation | Journal: Plos Pathog. / Year: 2011 Title: Membrane remodeling by the double-barrel scaffolding protein of poxvirus. Authors: Hyun, J.K. / Accurso, C. / Hijnen, M. / Schult, P. / Pettikiriarachchi, A. / Mitra, A.K. / Coulibaly, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3saq.cif.gz | 381.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3saq.ent.gz | 315.2 KB | Display | PDB format |
PDBx/mmJSON format | 3saq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3saq_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3saq_full_validation.pdf.gz | 452.9 KB | Display | |
Data in XML | 3saq_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 3saq_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/3saq ftp://data.pdbj.org/pub/pdb/validation_reports/sa/3saq | HTTPS FTP |
-Related structure data
Related structure data | 3samC 2samS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 65050.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Strain: Western Reserve / Gene: D13, D13L, VACWR118 / Plasmid: pPROEX-Hta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P68440 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.72 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: 200mM NaBr, 20% PEG3550, Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2010 |
Radiation | Monochromator: Double crystal monochromator with sagitally bent 2nd crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. all: 14242 / Num. obs: 13943 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 58.89 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 3.5→3.62 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.19 / Num. unique all: 1391 / % possible all: 98.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2SAM Resolution: 3.51→26.81 Å / Cor.coef. Fo:Fc: 0.7685 / Cor.coef. Fo:Fc free: 0.6864 / Isotropic thermal model: TLS with one group per chain / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ONLY TLS REFINEMENT (2 GROUPS). NO INDIVIDUAL B REFINEMENT DUE TO THE LOW RESOLUTION.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.15 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.79 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.51→26.81 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.51→3.79 Å / Total num. of bins used: 7
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|