+Open data
-Basic information
Entry | Database: PDB / ID: 4idu | ||||||
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Title | crystal structure of Schmallenberg virus nucleoprotein | ||||||
Components | (SBV nucleoprotein) x 2 | ||||||
Keywords | DNA BINDING PROTEIN / Schmallenberg virus / nucleoprotein / Protect genome RNA / replication and transcription | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Schmallenberg virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.08 Å | ||||||
Authors | Dong, H. / Li, P. / Elliott, R.M. / Dong, C. | ||||||
Citation | Journal: J.Virol. / Year: 2013 Title: Structure of Schmallenberg orthobunyavirus nucleoprotein suggests a novel mechanism of genome encapsidation Authors: Dong, H. / Li, P. / Elliott, R.M. / Dong, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4idu.cif.gz | 351.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4idu.ent.gz | 296.3 KB | Display | PDB format |
PDBx/mmJSON format | 4idu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/4idu ftp://data.pdbj.org/pub/pdb/validation_reports/id/4idu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26208.291 Da / Num. of mol.: 3 / Fragment: UNP residues 2-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schmallenberg virus / Gene: N / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: H2AM13 #2: Protein | | Mass: 26302.082 Da / Num. of mol.: 1 / Fragment: UNP residues 2-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schmallenberg virus / Gene: N / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: H2AM13 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.46 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M sodium formate, 20% PEG3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9218 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 13, 2012 |
Radiation | Monochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9218 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→33.92 Å / Num. all: 18405 / Num. obs: 18304 / % possible obs: 99.4 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.09 / Net I/σ(I): 2 |
Reflection shell | Resolution: 3.06→3.16 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1260 / Rsym value: 0.76 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.08→29.71 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.811 / SU B: 97.612 / SU ML: 0.799 / Cross valid method: THROUGHOUT / ESU R Free: 0.704 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 100.413 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.08→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.08→3.139 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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