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Yorodumi- PDB-3nma: Mutant P169S of Foot-and-mouth disease Virus RNA dependent RNA-po... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nma | ||||||
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Title | Mutant P169S of Foot-and-mouth disease Virus RNA dependent RNA-polymerase | ||||||
Components |
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Keywords | TRANSFERASE/RNA / Foot-and-mouth disease virus / 3D polymerase RNA-dependent RNA polymerase / picornavirus / Ribavirin / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / regulation of translation / protein complex oligomerization / monoatomic ion channel activity ...modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / 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 Similarity search - Function | ||||||
Biological species | Foot and mouth disease virus C | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Agudo, R. / Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Verdaguer, N. / Domingo, E. | ||||||
Citation | Journal: Plos Pathog. / Year: 2010 Title: A multi-step process of viral adaptation to a mutagenic nucleoside analogue by modulation of transition types leads to extinction-escape. Authors: Agudo, R. / Ferrer-Orta, C. / Arias, A. / de la Higuera, I. / Perales, C. / Perez-Luque, R. / 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 | 3nma.cif.gz | 108.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nma.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 3nma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/3nma ftp://data.pdbj.org/pub/pdb/validation_reports/nm/3nma | HTTPS FTP |
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-Related structure data
Related structure data | 3nkyC 3nl0C 4iqxC 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: 53418.609 Da / Num. of mol.: 1 / Mutation: P169S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot and mouth disease virus C / Strain: C-S8c1 / Plasmid: pET-28a (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q0QEE0, UniProt: Q9QCE4*PLUS |
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#2: RNA chain | Mass: 950.636 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: RNA chain | Mass: 565.406 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Chemical | ChemComp-MG / |
#5: 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: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 35% PEG 4000, 0.2M magnesium acetate, 0.1M sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 8, 2008 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 16296 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 18.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U09 Resolution: 2.6→19.42 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 26.742 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R Free: 0.335 / 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: 54.769 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20
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