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Open data
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Basic information
Entry | Database: PDB / ID: 3agq | ||||||
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Title | Structure of viral polymerase form II | ||||||
![]() | Elongation factor Ts, Elongation factor Tu 1, LINKER, Q beta replicase | ||||||
![]() | TRANSLATION / TRANSFERASE / RNA polymerase / replicase | ||||||
Function / homology | ![]() guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / response to antibiotic / RNA-dependent RNA polymerase activity / nucleotide binding / GTPase activity / GTP binding / RNA binding ...guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / response to antibiotic / RNA-dependent RNA polymerase activity / nucleotide binding / GTPase activity / GTP binding / RNA binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takeshita, D. / Tomita, K. | ||||||
![]() | ![]() Title: Assembly of Q{beta} viral RNA polymerase with host translational elongation factors EF-Tu and -Ts Authors: Takeshita, D. / Tomita, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243.6 KB | Display | ![]() |
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PDB format | ![]() | 191 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.9 KB | Display | ![]() |
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Full document | ![]() | 528.9 KB | Display | |
Data in XML | ![]() | 51.6 KB | Display | |
Data in CIF | ![]() | 69.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3agpSC 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: 141417.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Plasmid: pBAD33 / Production host: ![]() ![]() References: UniProt: P0A6P3, UniProt: P0A6N3, UniProt: Q8LTE0 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 32% PEG400, 0.2M magnesium acetate, 0.1M HEPES, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. obs: 28658 / % possible obs: 98.5 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.107 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.341 / Num. unique all: 1396 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AGP Resolution: 3.22→20 Å
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Refinement step | Cycle: LAST / Resolution: 3.22→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2213→3.2414 Å / Rfactor Rwork: 0.476 |