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Yorodumi- PDB-6gvv: Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mout... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gvv | ||||||
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Title | Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus | ||||||
Components | RNA polymerase 3D | ||||||
Keywords | VIRAL PROTEIN / RNA dependent RNA polymerase / Picornavirus / closed right hand conformation | ||||||
Function / homology | Function and homology information 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 | Foot-and-mouth disease virus - type C | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Verdaguer, N. / Ferrer Orta, C. | ||||||
Citation | Journal: J.Virol. / Year: 2018 Title: Contribution of a Multifunctional Polymerase Region of Foot-and-Mouth Disease Virus to Lethal Mutagenesis. Authors: de la Higuera, I. / Ferrer-Orta, C. / Moreno, E. / de Avila, A.I. / Soria, M.E. / Singh, K. / Caridi, F. / Sobrino, F. / Sarafianos, S.G. / Perales, C. / Verdaguer, N. / Domingo, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gvv.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gvv.ent.gz | 161.4 KB | Display | PDB format |
PDBx/mmJSON format | 6gvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gvv_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 6gvv_full_validation.pdf.gz | 442.9 KB | Display | |
Data in XML | 6gvv_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 6gvv_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/6gvv ftp://data.pdbj.org/pub/pdb/validation_reports/gv/6gvv | HTTPS FTP |
-Related structure data
Related structure data | 6gvyC 1u09S 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: 54050.219 Da / Num. of mol.: 1 / Mutation: M16A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type C / Production host: Escherichia coli (E. coli) References: UniProt: P03311, L-peptidase, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 2.43 Å3/Da / Density % sol: 49.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30% PEG 4000, 0.2M magnesium acetate, 0.1M MES[2-(N-morpholino) ethanesulfonic acid] pH 6.0 and 4% a-butyrolactone. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97166 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97166 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 22406 / % possible obs: 98.1 % / Redundancy: 8 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.35→2.48 Å / Rmerge(I) obs: 0.426 / Num. unique all: 2890 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U09 Resolution: 2.35→46.6 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 23.046 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.269 / 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: 56.695 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→46.6 Å
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