+Open data
-Basic information
Entry | Database: PDB / ID: 6r0g | ||||||
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Title | Getah virus macro domain in complex with ADPr, pose 2 | ||||||
Components | Non-structural polyprotein | ||||||
Keywords | VIRAL PROTEIN / Macro domain / Getah virus | ||||||
Function / homology | Function and homology information host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Getah virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Sulzenbacher, G. / Ferreira Ramos, A.S. / Coutard, B. | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Snapshots of ADP-ribose bound to Getah virus macro domain reveal an intriguing choreography. Authors: Ferreira-Ramos, A.S. / Sulzenbacher, G. / Canard, B. / Coutard, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r0g.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r0g.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 6r0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/6r0g ftp://data.pdbj.org/pub/pdb/validation_reports/r0/6r0g | HTTPS FTP |
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-Related structure data
Related structure data | 6qzuSC 6r0fC 6r0pC 6r0rC 6r0tC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 18120.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: synthetic gene / Source: (gene. exp.) Getah virus / Gene: nsP1234 / Plasmid: pDest14 Details (production host): from ThermoFischer, Gateway cloning Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: A0A143SL92, UniProt: Q5Y389*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: Imidazole-Malate pH 6,0 30% PEG 4K, 3 mM ADPr, 50 mM Glutamic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→42.35 Å / Num. obs: 36394 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 18.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.04 / Rrim(I) all: 0.069 / Rsym value: 0.055 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1913 / CC1/2: 0.527 / Rpim(I) all: 0.664 / Rrim(I) all: 1.127 / Rsym value: 0.905 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6QZU Resolution: 1.7→40.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.727 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.139 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→40.7 Å
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Refine LS restraints |
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