[English] 日本語
Yorodumi- PDB-3bbz: Structure of the nucleocapsid-binding domain from the mumps virus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bbz | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the nucleocapsid-binding domain from the mumps virus phosphoprotein | ||||||
Components | P protein | ||||||
Keywords | VIRAL PROTEIN / REPLICATION / molten globule | ||||||
Function / homology | P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha / BROMIDE ION / FORMIC ACID / Phosphoprotein Function and homology information | ||||||
Biological species | Mumps virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Kingston, R.L. / Gay, L.S. / Baase, W.S. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structure of the nucleocapsid-binding domain from the mumps virus polymerase; an example of protein folding induced by crystallization Authors: Kingston, R.L. / Gay, L.S. / Baase, W.S. / Matthews, B.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3bbz.cif.gz | 31 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3bbz.ent.gz | 21.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bbz_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3bbz_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 3bbz_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 3bbz_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/3bbz ftp://data.pdbj.org/pub/pdb/validation_reports/bb/3bbz | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 5455.335 Da / Num. of mol.: 2 / Fragment: nucleocapsid-binding domain, UNP residues 343-391 / Mutation: C356S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mumps virus / Strain: Jeryl-Lynn vaccine / Plasmid: pET41A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star (DE3) / References: UniProt: Q9J4L6 #2: Chemical | #3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.81 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.7 Details: 0.2M Alanine/KOH pH 9.7, 3.6-4.6M Ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 2.1→41.27 Å / Num. all: 4915 / Num. obs: 4915 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 5.8 | ||||||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.4 / Num. unique all: 484 / % possible all: 98.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.1→40.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.771 / SU ML: 0.154 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.318 / ESU R Free: 0.219 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.779 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→40.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Highest resolution: 2.1 Å / Num. reflection Rwork: 345 / Total num. of bins used: 20 |