[English] 日本語
Yorodumi- PDB-2fqm: Crystal structure of the oligomerization domain of the phosphopro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fqm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the oligomerization domain of the phosphoprotein of vesicular stomatitis virus | ||||||
Components | Phosphoprotein | ||||||
Keywords | VIRAL PROTEIN / negative strand RNA virus / polymerase / replication / cofactor | ||||||
Function / homology | Function and homology information virion component / host cell cytoplasm / RNA-dependent RNA polymerase activity Similarity search - Function | ||||||
Biological species | Vesicular stomatitis Indiana virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Ding, H. / Green, T.J. / Lu, S. / Luo, M. | ||||||
Citation | Journal: J.Virol. / Year: 2006 Title: Crystal structure of the oligomerization domain of the phosphoprotein of vesicular stomatitis virus Authors: Ding, H. / Green, T.J. / Lu, S. / Luo, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2fqm.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2fqm.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 2fqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fqm_validation.pdf.gz | 470.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2fqm_full_validation.pdf.gz | 486.6 KB | Display | |
Data in XML | 2fqm_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 2fqm_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/2fqm ftp://data.pdbj.org/pub/pdb/validation_reports/fq/2fqm | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer composed of molecule A and B. |
-Components
#1: Protein | Mass: 8442.568 Da / Num. of mol.: 6 / Mutation: L139M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vesicular stomatitis Indiana virus / Genus: Vesiculovirus / Strain: Indiana / Gene: P / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04880 #2: Water | ChemComp-HOH / | |
---|
-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 | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.32 Details: 2.48 M ammonium sulfate, 7% ethylene glycol, 0.05% n-octyl-b-D-glucopyranoside, pH 4.32, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 8, 2005 |
Radiation | Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 20435 / Num. obs: 20381 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.62 |
Reflection shell | Highest resolution: 2.3 Å / % possible all: 99.8 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|