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Open data
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Basic information
Entry | Database: PDB / ID: 4wyw | |||||||||
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Title | Mutant K20E of 3D polymerase from Foot-and-Mouth Disease Virus | |||||||||
![]() | RNA-directed RNA polymerase 3D-POL | |||||||||
![]() | TRANSFERASE / closed-right hand RNA dependent RNA polymerase Picornavirus | |||||||||
Function / homology | ![]() L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / regulation of translation ...L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ferrer-Orta, C. / Verdaguer, N. / de la Higuera, I. / Domingo, E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition. Authors: Ferrer-Orta, C. / de la Higuera, I. / Caridi, F. / Sanchez-Aparicio, M.T. / Moreno, E. / Perales, C. / Singh, K. / Sarafianos, S.G. / Sobrino, F. / 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 | ![]() | 114.1 KB | Display | ![]() |
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PDB format | ![]() | 85.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 769.5 KB | Display | ![]() |
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Full document | ![]() | 770.7 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wylC ![]() 4wzmC ![]() 4wzqC ![]() 4x2bC ![]() 1u09S 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: 54110.273 Da / Num. of mol.: 1 / Fragment: UNP RESDIUES 1830-2299 / Mutation: K20E Source method: isolated from a genetically manipulated source Details: This polymerase contain the mutation K20E / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-3PO / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% PEG4000, 0.2M Mg(CH3COO)2, 0.1M MES pH6.0, 4% gamma-butyrolactone PH range: 5.5-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.6 Å / Num. obs: 47356 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.15 |
Reflection shell | Resolution: 1.8→1.91 Å / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 3.5 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1U09 Resolution: 1.8→46.6 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.82 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.125 / 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: 25.72 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→46.6 Å
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Refine LS restraints |
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