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- PDB-3kmq: G62S mutant of foot-and-mouth disease virus RNA-polymerase in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kmq | ||||||
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Title | G62S mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA, tetragonal structure | ||||||
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![]() | TRANSFERASE/RNA / 3d / polymerase / rna dependent rna polymerase / ribavirin / foot-and-mouth disease virus / TRANSFERASE-RNA complex | ||||||
Function / homology | ![]() modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity ...modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / viral RNA genome replication / cysteine-type endopeptidase activity / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferrer-Orta, C. / Verdaguer, N. / Perez-Luque, R. | ||||||
![]() | ![]() Title: Structure of foot-and-mouth disease virus mutant polymerases with reduced sensitivity to ribavirin Authors: Ferrer-Orta, C. / Sierra, M. / Agudo, R. / de la Higuera, I. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.8 KB | Display | ![]() |
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PDB format | ![]() | 84.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.1 KB | Display | ![]() |
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Full document | ![]() | 463.3 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3klvC ![]() 3kmsC ![]() 3knaC ![]() 3koaC ![]() 1wneS 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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Unit cell |
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Components
#1: Protein | Mass: 53516.711 Da / Num. of mol.: 1 / Mutation: G62S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: RNA chain | Mass: 1601.024 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: RNA chain | Mass: 1561.000 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % / Description: The file contains Friedel pairs. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 4000, 0.2M magnesium acetate, 0.1M HEPES pH 7.0, 4% butyrolactone, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2008 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 59922 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.063 / Rsym value: 0.074 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Mean I/σ(I) obs: 3 / Num. unique all: 36423 / Rsym value: 0.49 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1wne Resolution: 2.11→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.164 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The file contains Friedel pairs.
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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: 48.983 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.164 Å / Total num. of bins used: 20
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