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Yorodumi- PDB-4tyb: An Ligand-observed Mass Spectrometry-based Approach Integrated in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tyb | ||||||
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Title | An Ligand-observed Mass Spectrometry-based Approach Integrated into the Fragment Based Lead Discovery Pipeline | ||||||
Components | Polyprotein | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / NS5B / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information serine-type peptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / fusion of virus membrane with host endosome membrane / ATP hydrolysis activity / proteolysis / RNA binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.93 Å | ||||||
Authors | Shui, W. / Yang, C. / Lin, J. / Chen, X. / Qin, S. / Chen, S. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: A ligand-observed mass spectrometry approach integrated into the fragment based lead discovery pipeline Authors: Chen, X. / Qin, S. / Chen, S. / Li, J. / Li, L. / Wang, Z. / Wang, Q. / Lin, J. / Yang, C. / Shui, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tyb.cif.gz | 413.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tyb.ent.gz | 339.8 KB | Display | PDB format |
PDBx/mmJSON format | 4tyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tyb_validation.pdf.gz | 476.7 KB | Display | wwPDB validaton report |
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Full document | 4tyb_full_validation.pdf.gz | 501.1 KB | Display | |
Data in XML | 4tyb_validation.xml.gz | 71.6 KB | Display | |
Data in CIF | 4tyb_validation.cif.gz | 97 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/4tyb ftp://data.pdbj.org/pub/pdb/validation_reports/ty/4tyb | HTTPS FTP |
-Related structure data
Related structure data | 4txsC 4ty8C 4ty9C 4tyaC 4txf C: citing same article (ref.) |
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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: 62791.984 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Production host: Escherichia coli (E. coli) / References: UniProt: D0PY27, RNA-directed RNA polymerase #2: Chemical | ChemComp-3B1 / ( |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.92 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: PEG4000, Dithiothreitol, 2-(N-morpholino)ethanesulfonic acid, Glycerin PH range: 5.5-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5415 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 23, 2012 |
Radiation | Monochromator: Cu filter / Protocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5415 Å / Relative weight: 1 |
Reflection | Resolution: 2.93→50 Å / Num. obs: 57886 / % possible obs: 99.2 % / Redundancy: 4.9 % / Net I/σ(I): 14.8 |
-Processing
Software |
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Refinement | Resolution: 2.93→47.41 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.848 / SU B: 18.05 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / 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: 28.21 Å2
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Refinement step | Cycle: 1 / Resolution: 2.93→47.41 Å
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Refine LS restraints |
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