[English] 日本語
Yorodumi- PDB-3sam: Structure of D13, the scaffolding protein of vaccinia virus (muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sam | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of D13, the scaffolding protein of vaccinia virus (mutant D513G) | ||||||
Components | Rifampicin resistance protein | ||||||
Keywords | VIRAL PROTEIN / Double-barrel / jelly-roll / Scaffolding protein / structural protein / rifampicin-resistance protein / Surface of the immature virions and viral crescents | ||||||
Function / homology | Poxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / FORMIC ACID / Scaffold protein OPG125 Function and homology information | ||||||
Biological species | Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.55 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 | 3sam.cif.gz | 341.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3sam.ent.gz | 276.4 KB | Display | PDB format |
PDBx/mmJSON format | 3sam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sam_validation.pdf.gz | 464.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3sam_full_validation.pdf.gz | 479.1 KB | Display | |
Data in XML | 3sam_validation.xml.gz | 61.3 KB | Display | |
Data in CIF | 3sam_validation.cif.gz | 86.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/3sam ftp://data.pdbj.org/pub/pdb/validation_reports/sa/3sam | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 64992.809 Da / Num. of mol.: 3 / Mutation: D513G 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 #2: Chemical | ChemComp-FMT / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.78 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.3M Na formate, 100mM Bis-Tris pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953689 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 16, 2011 |
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: 0.953689 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. all: 88239 / Num. obs: 87870 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 64.97 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 26.25 |
Reflection shell | Resolution: 2.55→2.62 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.1017 / Mean I/σ(I) obs: 2.25 / Num. unique all: 6430 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.55→17.99 Å / Cor.coef. Fo:Fc: 0.9524 / Cor.coef. Fo:Fc free: 0.9414 Isotropic thermal model: Individual B factors with coupling of bonded atoms Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.49 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.282 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→17.99 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.55→2.62 Å / Total num. of bins used: 20
|