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Yorodumi- PDB-6gp9: Structural studies of hepatitis C virus non-structural protein-5b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gp9 | ||||||
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Title | Structural studies of hepatitis C virus non-structural protein-5b of genotype 4a | ||||||
Components | RNA-directed RNA polymerase | ||||||
Keywords | TRANSFERASE / Hepatitic C virus / Genotype 4a / non structural 5 b (NS5b) protein | ||||||
Function / homology | Function and homology information membrane => GO:0016020 / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / fusion of virus membrane with host endosome membrane / RNA binding Similarity search - Function | ||||||
Biological species | Hepacivirus C | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Janowski, R. / Geber, H. / Protzer, U. / Niessing, D. | ||||||
Citation | Journal: Biorxiv / Year: 2022 Title: Structural studies of hepatitis C virus non-structural protein-5b of genotype 4a Authors: Gaber, H. / Niessing, D. / Protzer, U. / Janowski, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gp9.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gp9.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 6gp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gp9_validation.pdf.gz | 419.3 KB | Display | wwPDB validaton report |
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Full document | 6gp9_full_validation.pdf.gz | 426.8 KB | Display | |
Data in XML | 6gp9_validation.xml.gz | 21 KB | Display | |
Data in CIF | 6gp9_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/6gp9 ftp://data.pdbj.org/pub/pdb/validation_reports/gp/6gp9 | HTTPS FTP |
-Related structure data
Related structure data | 1c2pS 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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-Components
#1: Protein | Mass: 64050.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepacivirus C / Production host: Escherichia coli (E. coli) / References: UniProt: Q506M7, RNA-directed RNA polymerase |
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#2: 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: 2.08 Å3/Da / Density % sol: 40.86 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 100 mM sodium citrate pH 5.4, 25-30% (v/v) PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.965 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→100 Å / Num. obs: 10145 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 77.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.23 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 742 / CC1/2: 0.713 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C2P Resolution: 3.1→64.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.897 / SU B: 27.846 / SU ML: 0.453 / Cross valid method: THROUGHOUT / ESU R Free: 0.545
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70 Å2
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Refinement step | Cycle: 1 / Resolution: 3.1→64.7 Å
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Refine LS restraints |
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