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Open data
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Basic information
Entry | Database: PDB / ID: 6r0f | ||||||
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Title | Getah virus macro domain in complex with ADPr, pose 1 | ||||||
![]() | 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 | ![]() | 80.2 KB | Display | ![]() |
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PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qzuSC ![]() 6r0gC ![]() 6r0pC ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 1 - 160 / Label seq-ID: 3 - 162
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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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.9 Details: imidazole-Malate pH 5,9 34% PEG 4K, 3mM ADPr, 3 hours soaking with crystallization solutution additioned 15mM 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: 2.05→42.23 Å / Num. obs: 21125 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 25.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.097 / Rrim(I) all: 0.16 / Rsym value: 0.27 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.206 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1628 / CC1/2: 0.468 / Rpim(I) all: 0.908 / Rrim(I) all: 1.517 / Rsym value: 1.206 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QZU Resolution: 2.05→40.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.923 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.181 / 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 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→40.66 Å
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Refine LS restraints |
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