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Yorodumi- PDB-3qid: Crystal structures and functional analysis of murine norovirus RN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qid | ||||||
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Title | Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase | ||||||
Components | RNA dependent RNA polymeraseRNA-dependent RNA polymerase | ||||||
Keywords | TRANSFERASE / RNA POLYMERASE / VIRAL REPLICATION ENZYME | ||||||
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 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kim, K.H. / Intekhab, A. / Lee, J.H. | ||||||
Citation | Journal: J.Gen.Virol. / Year: 2011 Title: Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase. Authors: Lee, J.H. / Alam, I. / Han, K.R. / Cho, S. / Shin, S. / Kang, S. / Yang, J.M. / Kim, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qid.cif.gz | 308.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qid.ent.gz | 250.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/3qid ftp://data.pdbj.org/pub/pdb/validation_reports/qi/3qid | HTTPS FTP |
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-Related structure data
Related structure data | 1sh2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58519.539 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murine norovirus 1 / Gene: MNV RdRp / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q80J95 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.26M (NH4)2SO4, 100mM cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 78636 / % possible obs: 99.2 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 21.5 / Num. unique all: 78636 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SH2 Resolution: 2.5→49.07 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 8.167 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 119.41 Å2 / Biso mean: 30.1367 Å2 / Biso min: 3.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→49.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.503→2.568 Å / Total num. of bins used: 20
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