+Open data
-Basic information
Entry | Database: PDB / ID: 4xzc | ||||||
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Title | The crystal structure of Kupe virus nucleoprotein | ||||||
Components | Nucleoprotein | ||||||
Keywords | RNA BINDING PROTEIN / nucleoprotein / Kupe virus | ||||||
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 | Kupe virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 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 | 4xzc.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xzc.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/4xzc ftp://data.pdbj.org/pub/pdb/validation_reports/xz/4xzc | HTTPS FTP |
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-Related structure data
Related structure data | 4xz8C 4xzaC 4xzeC 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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Unit cell |
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-Components
#1: Protein | Mass: 54188.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kupe virus / Production host: Escherichia coli (E. coli) / References: UniProt: B8PWH3 #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: 2.68 Å3/Da / Density % sol: 54.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 200mM sodium nitrate (PH 8.0), 5mM cobalt chloride, 8% (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: 2.6→50 Å / Num. obs: 37285 / % possible obs: 98.5 % / Redundancy: 11.3 % / Net I/σ(I): 20.92 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 10 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.296 / Num. measured obs: 19 / Rsym value: 0.42 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U3I Resolution: 2.601→49.059 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.601→49.059 Å
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Refine LS restraints |
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LS refinement shell |
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