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Yorodumi- PDB-3klv: M296I G62S mutant of foot-and-mouth disease virus RNA-polymerase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3klv | ||||||
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Title | M296I G62S mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA | ||||||
Components |
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Keywords | Transferase/RNA / FMDV / RNA dependent RNA polymerase / RTP / Transferase-RNA complex | ||||||
Function / homology | Function and homology information modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell ...modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Foot-and-mouth disease virus - type C | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Ferrer-Orta, C. / Sierra, M. / Agudo, R. / Perez-Luque, R. / Arias, A. / Verdaguer, N. | ||||||
Citation | Journal: J.Virol. / Year: 2010 Title: Structure of foot-and-mouth disease virus mutant polymerases with reduced sensitivity to ribavirin Authors: Ferrer-Orta, C. / Sierra, M. / Agudo, R. / de la Higuera, I. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3klv.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3klv.ent.gz | 171 KB | Display | PDB format |
PDBx/mmJSON format | 3klv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/3klv ftp://data.pdbj.org/pub/pdb/validation_reports/kl/3klv | HTTPS FTP |
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-Related structure data
Related structure data | 3kmqC 3kmsC 3knaC 3koaC 1wneS S: Starting model for refinement 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: 53498.672 Da / Num. of mol.: 1 / Mutation: G62S M296I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type C / Gene: 3D / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9QCE3, RNA-directed RNA polymerase | ||
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#2: RNA chain | Mass: 2236.395 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: RNA chain | Mass: 1561.000 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#4: Chemical | #5: 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: 2.2 Å3/Da / Density % sol: 44.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 28% PEG 4000, 0.1M HEPES, 4% butyrolactone, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 15634 / % possible obs: 75 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WNE Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.874 / SU B: 33.333 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / 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: 65.637 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.494 Å / Origin y: 26.868 Å / Origin z: 23.912 Å
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Refinement TLS group |
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