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- PDB-5n8x: Trigonal structure of mutant V173I of 3D polymerase from Foot-and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n8x | ||||||
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Title | Trigonal structure of mutant V173I of 3D polymerase from Foot-and-Mouth Disease Virus | ||||||
![]() | 3D polymerase | ||||||
![]() | VIRAL PROTEIN / 3Dpolymerase / RNA dependent RNA polymerases / 5'-fluoracil / nucleotide analogues | ||||||
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 / cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...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 / 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. | ||||||
![]() | ![]() Title: Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus. Authors: de la Higuera, I. / Ferrer-Orta, C. / de Avila, A.I. / Perales, C. / Sierra, M. / Singh, K. / Sarafianos, S.G. / Dehouck, Y. / Bastolla, U. / Verdaguer, N. / Domingo, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.1 KB | Display | ![]() |
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PDB format | ![]() | 163.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.9 KB | Display | ![]() |
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Full document | ![]() | 451.6 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n95C ![]() 1wnrS 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: 54124.367 Da / Num. of mol.: 1 / Mutation: V173I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-MN / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 36% PEG 4000, 0.2M ammonium acetate 0.1M MES(2-(N-morpholino) ethanesulfonic acid) pH 6.0 4% gamma-butyrolactone. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.75 Å / Num. obs: 20009 / % possible obs: 96.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2782 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WNR Resolution: 2.4→46.75 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 26.761 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.604 / ESU R Free: 0.307 / 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: 73.103 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→46.75 Å
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Refine LS restraints |
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