+Open data
-Basic information
Entry | Database: PDB / ID: 5a97 | ||||||
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Title | Hazara virus nucleocapsid protain | ||||||
Components | NUCLEOCAPSID PROTEINVirus | ||||||
Keywords | VIRAL PROTEIN / HAZARA / NUCLEOCAPSID | ||||||
Function / homology | Function and homology information helical viral capsid / viral nucleocapsid / Hydrolases; Acting on ester bonds / hydrolase activity / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | HAZARA VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Surtees, R. / Ariza, A. / Hewson, R. / Barr, J.N. / Edwards, T.A. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2015 Title: The Crystal Structure of the Hazara Virus Nucleocapsid Protein. Authors: Surtees, R. / Ariza, A. / Punch, E.K. / Trinh, C.H. / Dowall, S.D. / Hewson, R. / Hiscox, J.A. / Barr, J.N. / Edwards, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a97.cif.gz | 527.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a97.ent.gz | 443.4 KB | Display | PDB format |
PDBx/mmJSON format | 5a97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/5a97 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/5a97 | HTTPS FTP |
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-Related structure data
Related structure data | 4aklS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 54642.137 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HAZARA VIRUS / Strain: JC280 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: M4PWE6, UniProt: P27318*PLUS #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: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 5 Details: 15% PEG 10,000, 0.1 M SODIUM CITRATE PH 5, 0.1 M NACL, 2 % DIOXANE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97779 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Jun 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97779 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→65.25 Å / Num. obs: 74079 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.7 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AKL Resolution: 2.7→224.64 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.898 / SU B: 22.904 / SU ML: 0.368 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
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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: 85.501 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→224.64 Å
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Refine LS restraints |
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