+Open data
-Basic information
Entry | Database: PDB / ID: 4bgp | ||||||
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Title | Crystal structure of La Crosse virus nucleoprotein | ||||||
Components | NUCLEOPROTEIN | ||||||
Keywords | VIRAL PROTEIN / ORTHOBUNYAVIRUS / NUCLEOPROTEIN | ||||||
Function / homology | Function and homology information helical viral capsid / viral nucleocapsid / ribonucleoprotein complex / symbiont-mediated suppression of host gene expression / RNA binding Similarity search - Function | ||||||
Biological species | LA CROSSE VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Reguera, J. / Malet, H. / Weber, F. / Cusack, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structural Basis for Encapsidation of Genomic RNA by La Crosse Orthobunyavirus Nucleoprotein Authors: Reguera, J. / Malet, H. / Weber, F. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bgp.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bgp.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 4bgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/4bgp ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bgp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26696.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: EXTRA G AT N-TERMINUS AFTER HIS-TAG CLEAVAGE / Source: (gene. exp.) LA CROSSE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04873 | ||||
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#2: Chemical | ChemComp-GOL / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | EXTRA G AT N-TERMINUS AFTER HIS-TAG CLEAVAGE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 0.2 M LISO4, 0.1 M TRIS-HCL PH 8.5, 15% W/V PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 29488 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.97 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.72 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.8→46.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.171 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY
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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: 28.342 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.92 Å
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