+Open data
-Basic information
Entry | Database: PDB / ID: 3agq | ||||||
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Title | Structure of viral polymerase form II | ||||||
Components | Elongation factor Ts, Elongation factor Tu 1, LINKER, Q beta replicase | ||||||
Keywords | TRANSLATION / TRANSFERASE / RNA polymerase / replicase | ||||||
Function / homology | Function and homology information guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / response to antibiotic / GTPase activity / GTP binding / RNA binding ...guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / response to antibiotic / GTPase activity / GTP binding / RNA binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) synthetic construct (others) Escherichia phage Qbeta (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å | ||||||
Authors | Takeshita, D. / Tomita, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3agq.cif.gz | 243.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3agq.ent.gz | 191 KB | Display | PDB format |
PDBx/mmJSON format | 3agq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/3agq ftp://data.pdbj.org/pub/pdb/validation_reports/ag/3agq | HTTPS FTP |
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-Related structure data
Related structure data | 3agpSC 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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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.) Escherichia coli O157:H7 (bacteria), (gene. exp.) synthetic construct (others), (gene. exp.) Escherichia phage Qbeta (virus) Plasmid: pBAD33 / Production host: Escherichia coli (E. coli) References: UniProt: P0A6P3, UniProt: P0A6N3, UniProt: Q8LTE0 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |