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Yorodumi- PDB-2f8e: Foot and Mouth Disease Virus RNA-dependent RNA polymerase in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f8e | ||||||
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Title | Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with uridylylated VPg protein | ||||||
Components |
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Keywords | TRANSFERASE / Foot and Mouth Disease Virus / RNA-dependent RNA polymerase / VPg protein / protein primer | ||||||
Function / homology | Function and homology information T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / viral RNA genome replication ...T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Foot-and-mouth disease virus - type C | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: The structure of a protein primer-polymerase complex in the initiation of genome replication Authors: Ferrer-Orta, C. / Arias, A. / Agudo, R. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Structure of foot-and-mouth disease virus RNA-dependent RNA polymerase and its complex with a template-primer RNA Authors: Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / 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 | 2f8e.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f8e.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 2f8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f8e_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 2f8e_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 2f8e_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 2f8e_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/2f8e ftp://data.pdbj.org/pub/pdb/validation_reports/f8/2f8e | HTTPS FTP |
-Related 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: 53210.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type C / Genus: Aphthovirus / Species: Foot-and-mouth disease virus / Strain: c-s8c1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) References: GenBank: 6318192, UniProt: Q0QEE0*PLUS, RNA-directed RNA polymerase |
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#2: Protein/peptide | Mass: 2552.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: VPg was prepared by solid phase peptide synthesis / References: UniProt: Q9DS05*PLUS |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-MN / |
#5: Chemical | ChemComp-U5P / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 33% PEG4K, 0.2M ammonium acetate, 0.1M sodium citrate pH 5.6, 4% butyrolactone, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→81.65 Å / Num. all: 11795 / Num. obs: 11795 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Foot and Mouth disease Virus Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 51.876 / SU ML: 0.432 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.504 / 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: 60.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.898→2.973 Å / Total num. of bins used: 20
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