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Yorodumi- PDB-4aqf: X-ray crystallographic structure of Crimean-congo haemorrhagic fe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aqf | ||||||
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Title | X-ray crystallographic structure of Crimean-congo haemorrhagic fever virus nucleoprotein | ||||||
Components | (NUCLEOPROTEIN) x 2 | ||||||
Keywords | VIRAL PROTEIN / NAIROVIRUS | ||||||
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 | CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å | ||||||
Authors | Wang, Y. / Dutta, S. / Karlberg, H. / Devignot, S. / Weber, F. / Hao, Q. / Tan, Y.J. / Mirazimi, A. / Kotaka, M. | ||||||
Citation | Journal: J.Virol. / Year: 2012 Title: Structure of Crimean-Congo Haemorraghic Fever Virus Nucleoprotein: Superhelical Homo-Oligomers and the Role of Caspase-3 Cleavage. Authors: Wang, Y. / Dutta, S. / Karlberg, H. / Devignot, S. / Weber, F. / Hao, Q. / Tan, Y.J. / Mirazimi, A. / Kotaka, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aqf.cif.gz | 584.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aqf.ent.gz | 488.4 KB | Display | PDB format |
PDBx/mmJSON format | 4aqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/4aqf ftp://data.pdbj.org/pub/pdb/validation_reports/aq/4aqf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 54031.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS / Strain: IBAR10200 / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P89522 #2: Protein | | Mass: 54045.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS / Strain: IBAR10200 / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): RIL / References: UniProt: P89522 #3: Chemical | ChemComp-SO4 / #4: 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: 4.55 Å3/Da / Density % sol: 72.96 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M MES, PH 6.5, 37% (V/V) PEG 200, 12% (V/V) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 54514 / % possible obs: 99.9 % / Observed criterion σ(I): -1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 3.1→29.24 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU B: 35.36 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / 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: 96.484 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→29.24 Å
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Refine LS restraints |
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