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- PDB-6r0p: Getah virus macro domain in complex with ADPr in double open conf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r0p | ||||||
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Title | Getah virus macro domain in complex with ADPr in double open conformation | ||||||
![]() | Non-structural polyprotein | ||||||
![]() | VIRAL PROTEIN / Macro domain / Getah virus | ||||||
Function / homology | ![]() host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 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 / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sulzenbacher, G. / Ferreira Ramos, A.S. / Coutard, B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.6 KB | Display | ![]() |
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PDB format | ![]() | 63.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qzuSC ![]() 6r0fC ![]() 6r0gC ![]() 6r0rC ![]() 6r0tC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 18120.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: synthetic gene / Source: (gene. exp.) ![]() Details (production host): from ThermoFischer, Gateway cloning Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: Imidazole-Malate pH 6.0, 32% PEG 4K, 3mM ADPr, 30mM Aspartic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.6→40.83 Å / Num. obs: 44233 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 15.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.043 / Rrim(I) all: 0.069 / Rsym value: 0.053 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.119 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2174 / CC1/2: 0.559 / Rpim(I) all: 0.915 / Rrim(I) all: 1.451 / Rsym value: 1.119 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QZU Resolution: 1.6→36.41 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.841 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.083 / 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: 25.39 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→36.41 Å
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Refine LS restraints |
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