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- PDB-6s2l: FMDV 3D polymerase crystallized in presence of (F)uridylylated VP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6s2l | ||||||
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Title | FMDV 3D polymerase crystallized in presence of (F)uridylylated VPg peptide | ||||||
![]() | Genome polyprotein | ||||||
![]() | VIRAL PROTEIN / RNA dependent RNA polymerase 3D polymerase VPg 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 | ![]() ![]() ![]() | ||||||
![]() | Verdaguer, N. / Ferrer-Orta, C. | ||||||
![]() | ![]() Title: (F)uridylylated Peptides Linked to VPg1 of Foot-and- Mouth Disease Virus (FMDV): Design, Synthesis and X-Ray Crystallography of the Complexes with FMDV RNA-Dependent RNA Polymerase. Authors: de Castro, S. / Ferrer-Orta, C. / Mills, A. / Fernandez-Cureses, G. / Gago, F. / Verdaguer, N. / Camarasa, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.4 KB | Display | ![]() |
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PDB format | ![]() | 160 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.1 KB | Display | ![]() |
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Full document | ![]() | 441.8 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u09S S: Starting model for refinement |
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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: 54110.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate -/Spain/S8c1SantaPau/1970 serotype C Production host: ![]() ![]() References: UniProt: P03311, L-peptidase, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M ammonium acetate, 30% PEG 4K, 0.1M MES pH 6.0, 4 butyrolactone |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97692 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→74.23 Å / Num. obs: 24747 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.039 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3536 / Rpim(I) all: 0.319 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1U09 Resolution: 2.3→74.23 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 15.637 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.241 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.302 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→74.23 Å
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Refine LS restraints |
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