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Yorodumi- PDB-3ur0: Crystal structures of murine norovirus RNA-dependent RNA polymera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ur0 | ||||||
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Title | Crystal structures of murine norovirus RNA-dependent RNA polymerase in complex with Suramin | ||||||
Components | RNA-dependent RNA polymerase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / RNA-dependent RNA polymerase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | murine norovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Milani, M. / Mastrangelo, E. / Bolognesi, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structure-Based Inhibition of Norovirus RNA-Dependent RNA Polymerases. Authors: Mastrangelo, E. / Pezzullo, M. / Tarantino, D. / Petazzi, R. / Germani, F. / Kramer, D. / Robel, I. / Rohayem, J. / Bolognesi, M. / Milani, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ur0.cif.gz | 592.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ur0.ent.gz | 507.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ur0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/3ur0 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/3ur0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 58435.422 Da / Num. of mol.: 3 / Fragment: UNP residues 1181-1687 Source method: isolated from a genetically manipulated source Source: (gene. exp.) murine norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q80J95 #2: Chemical | ChemComp-SO4 / #3: Chemical | #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: 3.36 Å3/Da / Density % sol: 63.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 1.3M ammonium sulfate, 10% glycerol, 0.1M TRIS, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 29, 2011 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→48 Å / Num. all: 82297 / Num. obs: 82297 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.45→2.58 Å / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→48 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / SU B: 20.235 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.265 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.307 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.452→2.516 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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