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Yorodumi- PDB-4wzq: Mutant K20E of RNA dependent RNA polymerase 3D from Foot-and-Mout... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wzq | ||||||
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Title | Mutant K20E of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus complexed with RNA | ||||||
Components |
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Keywords | TRANSFERASE / RNA dependent RNA polymerase / Nuclear Localization Signal / Picornavirus / closed right-hand | ||||||
Function / homology | Function and homology information L-peptidase / modulation by virus of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization ...L-peptidase / modulation by virus of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / regulation of translation / monoatomic ion channel activity / 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 / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Foot-and-mouth disease virus synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Verdaguer, N. / Ferrer-Orta, C. | ||||||
Citation | Journal: J.Virol. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wzq.cif.gz | 221.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wzq.ent.gz | 176.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/4wzq ftp://data.pdbj.org/pub/pdb/validation_reports/wz/4wzq | HTTPS FTP |
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-Related structure data
Related structure data | 4wylC 4wywC 4wzmC 4x2bC 1wneS 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: 54177.340 Da / Num. of mol.: 1 / Fragment: UNP residues 1858-2328 / Mutation: K20E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus / Gene: CDS / Plasmid: pET28a Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A4H1Z0, UniProt: P03311*PLUS |
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#2: RNA chain | Mass: 2541.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: RNA chain | Mass: 2212.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-MN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30%PEG 4000, 0.2M Mg(CH3COO)2, 0.1M MES pH6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.5 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→43.16 Å / Num. obs: 13460 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1wne Resolution: 2.8→43.16 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.885 / SU B: 41.101 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / 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: 73.586 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→43.16 Å
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Refine LS restraints |
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