+Open data
-Basic information
Entry | Database: PDB / ID: 4xze | ||||||
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Title | The crystal structure of Hazara virus nucleoprotein | ||||||
Components | Nucleoprotein | ||||||
Keywords | RNA BINDING PROTEIN / nucleoprotein / Hazara virus | ||||||
Function / homology | Nucleocapsid N protein / Nucleocapsid N protein / helical viral capsid / viral nucleocapsid / Hydrolases; Acting on ester bonds / hydrolase activity / ribonucleoprotein complex / RNA binding / Nucleoprotein Function and homology information | ||||||
Biological species | Hazara virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Guo, Y. / Wang, W. / Liu, X. / Wang, X. / Wang, J. / Huo, T. / Liu, B. | ||||||
Citation | Journal: J.Virol. / Year: 2015 Title: Structural and Functional Diversity of Nairovirus-Encoded Nucleoproteins. Authors: Wang, W. / Liu, X. / Wang, X. / Dong, H. / Ma, C. / Wang, J. / Liu, B. / Mao, Y. / Wang, Y. / Li, T. / Yang, C. / Guo, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xze.cif.gz | 369.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xze.ent.gz | 302.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xze_validation.pdf.gz | 468.6 KB | Display | wwPDB validaton report |
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Full document | 4xze_full_validation.pdf.gz | 515.9 KB | Display | |
Data in XML | 4xze_validation.xml.gz | 68.1 KB | Display | |
Data in CIF | 4xze_validation.cif.gz | 92.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/4xze ftp://data.pdbj.org/pub/pdb/validation_reports/xz/4xze | HTTPS FTP |
-Related structure data
Related structure data | 4xz8C 4xzaC 4xzcC 3u3iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 54545.023 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hazara virus / Production host: Escherichia coli (E. coli) / References: UniProt: M4PWE6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 200mM potassium citrate tribasic monohydrate (PH 8.0), 5mM manganese chloride,14% (wt/vol) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 42788 / % possible obs: 84.7 % / Redundancy: 6 % / Net I/σ(I): 11.008 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 0.327 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U3I Resolution: 2.9→48.22 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.18 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.9→48.22 Å
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Refine LS restraints |
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LS refinement shell |
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