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Yorodumi- PDB-5dsd: The crystal structure of the C-terminal domain of Ebola (Bundibug... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dsd | |||||||||
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Title | The crystal structure of the C-terminal domain of Ebola (Bundibugyo) nucleoprotein | |||||||||
Components | Nucleoprotein | |||||||||
Keywords | VIRAL PROTEIN / Filoviridae | |||||||||
Function / homology | P40 nucleoprotein, subdomain 2, Borna disease virus / Ebola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / Nucleoprotein Function and homology information | |||||||||
Biological species | Bundibugyo virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | |||||||||
Authors | Baker, L. / Handing, K.B. / Utepbergenov, D. / Derewenda, U. / Derewenda, Z.S. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Molecular architecture of the nucleoprotein C-terminal domain from the Ebola and Marburg viruses. Authors: Baker, L.E. / Ellena, J.F. / Handing, K.B. / Derewenda, U. / Utepbergenov, D. / Engel, D.A. / Derewenda, Z.S. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2014 Title: The structure of the C-terminal domain of the Zaire ebolavirus nucleoprotein. Authors: Dziubanska, P.J. / Derewenda, U. / Ellena, J.F. / Engel, D.A. / Derewenda, Z.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dsd.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dsd.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dsd_validation.pdf.gz | 428.4 KB | Display | wwPDB validaton report |
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Full document | 5dsd_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | 5dsd_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 5dsd_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/5dsd ftp://data.pdbj.org/pub/pdb/validation_reports/ds/5dsd | HTTPS FTP |
-Related structure data
Related structure data | 5e2xC 4qb0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 12267.726 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 641-739) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bundibugyo virus / Gene: NP, DH33_45404gpNP / Plasmid: Parallel1-MBPHis / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: B8XCM7 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.94 Å3/Da / Density % sol: 79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Crystallization solution: 1.33 M LiSO4, 0.1 M Tris pH 8.5. 1:1 ratio (250 nL: 250 nL) of precipitant to protein (at a concentration of 13.9 mg/ml). 60 mcL reservoir. Protein purification ...Details: Crystallization solution: 1.33 M LiSO4, 0.1 M Tris pH 8.5. 1:1 ratio (250 nL: 250 nL) of precipitant to protein (at a concentration of 13.9 mg/ml). 60 mcL reservoir. Protein purification buffer 50mM Tris-HCl, 150 mM NaCl; pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 14, 2014 |
Diffraction measurement | Details: 0.50 degrees, -1.0 sec, detector distance 350.62 mm Method: \w scans |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.084 / Number: 184210 |
Reflection | Resolution: 2.3→80 Å / Num. obs: 12398 / % possible obs: 94.3 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.084 / Net I/av σ(I): 31.34 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.432 / % possible all: 64.7 |
Cell measurement | Reflection used: 184210 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QB0 Resolution: 2.31→80 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.2071 / WRfactor Rwork: 0.1698 / FOM work R set: 0.8163 / SU B: 9.71 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1436 / SU Rfree: 0.1412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 243.89 Å2 / Biso mean: 81.78 Å2 / Biso min: 46.22 Å2
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Refinement step | Cycle: final / Resolution: 2.31→80 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.312→2.372 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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