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Yorodumi- PDB-5vkd: Crystal structure of C-terminal domain of Ebola (Bundibugyo) nucl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vkd | ||||||
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Title | Crystal structure of C-terminal domain of Ebola (Bundibugyo) nucleoprotein in complex with Fab fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ebolavirus / Nucleoprotein / Fab / antibody fragment | ||||||
Function / homology | Function and homology information viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Bundibugyo ebolavirus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å | ||||||
Authors | Radwanska, M.J. / Derewenda, U. / Kossiakoff, A. / Derewenda, Z.S. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: The structure of the C-terminal domain of the nucleoprotein from the Bundibugyo strain of the Ebola virus in complex with a pan-specific synthetic Fab. Authors: Radwanska, M.J. / Jaskolowski, M. / Davydova, E. / Derewenda, U. / Miyake, T. / Engel, D.A. / Kossiakoff, A.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 | 5vkd.cif.gz | 215.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vkd.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/5vkd ftp://data.pdbj.org/pub/pdb/validation_reports/vk/5vkd | 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: 12267.726 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fragment: C-terminal domain (UNP residues 641-739) Gene Name(s): NP DH33_45404gpNP Source: (gene. exp.) Bundibugyo ebolavirus / Production host: Escherichia coli (E. coli) / References: UniProt: R4QJ68, UniProt: B8XCM7*PLUS |
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#2: Antibody | Mass: 25216.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#3: Antibody | Mass: 23258.783 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#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: 2.16 Å3/Da / Density % sol: 43.01 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium formate, 10% w/v Polyvinylpyrrolidone, 20% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: AREA DETECTOR / Date: Apr 17, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.749→42.88 Å / Num. obs: 53300 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 27.5 Å2 / Net I/σ(I): 1.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.749→41.471 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.749→41.471 Å
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Refine LS restraints |
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LS refinement shell |
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