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- PDB-3kna: M296I mutant of foot-and-mouth disease virus RNA-polymerase in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kna | ||||||
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Title | M296I mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA | ||||||
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![]() | Transferase/RNA / RNA dependent RNA polymerase / 3d polymerase / foot-and-mouth disease virus / ribavirin / Transferase-RNA complex | ||||||
Function / homology | ![]() modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / regulation of translation / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity ...modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / regulation of translation / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferrer-Orta, C. / Verdaguer, N. / Perez-Luque, R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.9 KB | Display | ![]() |
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PDB format | ![]() | 170.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.8 KB | Display | ![]() |
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Full document | ![]() | 470.8 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3klvC ![]() 3kmqC ![]() 3kmsC ![]() 3koaC ![]() 1wneS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53468.645 Da / Num. of mol.: 1 / Mutation: M296I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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 | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 4000, 0.1M HEPES pH 7.0, 4% butyrolactone, 0.2M Magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2008 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→74 Å / Num. obs: 13868 / % possible obs: 99.5 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.11 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.7 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WNE Resolution: 2.8→74 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.875 / SU B: 37.117 / SU ML: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.444 / 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: 65.621 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.7407 Å / Origin y: 25.6187 Å / Origin z: 30.962 Å
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Refinement TLS group |
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