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Yorodumi- PDB-2wa2: Structure of the methyltransferase domain from Modoc Virus, a Fla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wa2 | ||||||
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Title | Structure of the methyltransferase domain from Modoc Virus, a Flavivirus with No Known Vector (NKV) | ||||||
Components | NON-STRUCTURAL PROTEIN 5 | ||||||
Keywords | TRANSFERASE / S-ADENOSYL-L- METHIONINE / VIRION / MEMBRANE / FLAVIVIRUS / MODOC VIRUS / N7-METHYLTRANSFERASE / 2'-O-METHYLTRANSFERASE / TRANSMEMBRANE / ENVELOPE PROTEIN / METHYLTRANSFERASE | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / proteolysis / RNA binding / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | MODOC VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Jansson, A.M. / Johansson, P. / Jones, T.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structure of the Methyltransferase Domain from the Modoc Virus, a Flavivirus with No Known Vector. Authors: Jansson, A.M. / Jakobsson, E. / Johansson, P. / Lantez, V. / Coutard, B. / De Lamballerie, X. / Unge, T. / Jones, T.A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wa2.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wa2.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wa2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/2wa2 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/2wa2 | HTTPS FTP |
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-Related structure data
Related structure data | 2wa1C 1l9kS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30812.219 Da / Num. of mol.: 2 / Fragment: NS5 PROTEIN, RESIDUES 2477-2744 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MODOC VIRUS / Plasmid: PCR T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q8QL64 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 2553 TO THR ENGINEERED RESIDUE IN CHAIN A, GLY 2563 TO SER ...ENGINEERED | Sequence details | THE UNIPROT ACCESSION NUMBER REFERS TO THE WHOLE POLYPROTEI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 45 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.07 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 45634 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.1 / % possible all: 63.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L9K Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.475 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.137 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.107 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40 Å
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