+Open data
-Basic information
Entry | Database: PDB / ID: 3u3i | ||||||
---|---|---|---|---|---|---|---|
Title | A RNA binding protein from Crimean-Congo hemorrhagic fever virus | ||||||
Components | Nucleocapsid protein | ||||||
Keywords | RNA BINDING PROTEIN / nucleocapsid protein / endonuclease / RNA binding / CCHFV | ||||||
Function / homology | Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1110 / Nucleocapsid N protein / Nucleocapsid N protein / helical viral capsid / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / viral nucleocapsid / Up-down Bundle / Mainly Alpha / Nucleocapsid protein Function and homology information | ||||||
Biological species | Crimean-Congo hemorrhagic fever virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.304 Å | ||||||
Authors | Guo, Y. / Wang, W.M. / Ji, W. / Deng, M. / Sun, Y.N. / Lou, Z.Y. / Rao, Z.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Crimean-Congo hemorrhagic fever virus nucleoprotein reveals endonuclease activity in bunyaviruses Authors: Guo, Y. / Wang, W.M. / Ji, W. / Deng, M. / Sun, Y.N. / Zhou, H. / Yang, C. / Deng, F. / Wang, H. / Hu, Z. / Lou, Z.Y. / Rao, Z.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3u3i.cif.gz | 206.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3u3i.ent.gz | 166.1 KB | Display | PDB format |
PDBx/mmJSON format | 3u3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u3i_validation.pdf.gz | 430.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3u3i_full_validation.pdf.gz | 470.9 KB | Display | |
Data in XML | 3u3i_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 3u3i_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/3u3i ftp://data.pdbj.org/pub/pdb/validation_reports/u3/3u3i | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53984.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q3HLI8 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.02 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: KCl, 20%(w/v) PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 22556 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.46 Å2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.304→43.639 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7912 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 26.96 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.356 Å2 / ksol: 0.275 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 209.3 Å2 / Biso mean: 49.847 Å2 / Biso min: 11.6 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.304→43.639 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|