+Open data
-Basic information
Entry | Database: PDB / ID: 4j4x | ||||||
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Title | Crystal structure of GraVN | ||||||
Components | NP protein | ||||||
Keywords | VIRAL PROTEIN / nucleocapsid protein / nucleoprotein | ||||||
Function / homology | Function and homology information host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / host cell nucleus / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Granada virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Jiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Zhu, Y. / Zhang, F. ...Jiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Zhu, Y. / Zhang, F. / Wang, T. / Li, C. / Zuo, X. / Luan, C.H. / Li, D. / Liu, Z.J. | ||||||
Citation | Journal: J.Virol. / Year: 2013 Title: Structure of severe Fever with thrombocytopenia syndrome virus nucleocapsid protein in complex with suramin reveals therapeutic potential Authors: Jiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Peng, Y. / Zhu, Y. / Zhang, F. / Wang, T. / Li, C. / Zuo, X. / Luan, C.H. / Li, D. / Liu, Z.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j4x.cif.gz | 290.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j4x.ent.gz | 240.3 KB | Display | PDB format |
PDBx/mmJSON format | 4j4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j4x_validation.pdf.gz | 476 KB | Display | wwPDB validaton report |
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Full document | 4j4x_full_validation.pdf.gz | 533.5 KB | Display | |
Data in XML | 4j4x_validation.xml.gz | 57.8 KB | Display | |
Data in CIF | 4j4x_validation.cif.gz | 80.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/4j4x ftp://data.pdbj.org/pub/pdb/validation_reports/j4/4j4x | HTTPS FTP |
-Related structure data
Related structure data | 4j4rSC 4j4sC 4j4uC 4j4vC 4j4wC 4j4yC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 28436.949 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Granada virus / Production host: Escherichia coli (E. coli) / References: UniProt: E2DQZ4 #2: Water | ChemComp-HOH / | |
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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: 2.61 Å3/Da / Density % sol: 52.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M MgCl2, 21% PEG 1000, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2012 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→49.64 Å / Num. all: 56301 / Num. obs: 54500 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.51→2.54 Å / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J4R Resolution: 2.51→49.59 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.911 / SU B: 0.011 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 58.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→49.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.505→2.57 Å / Total num. of bins used: 20
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