+Open data
-Basic information
Entry | Database: PDB / ID: 3avx | ||||||
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Title | Structure of viral RNA polymerase complex 5 | ||||||
Components |
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Keywords | TRANSLATION / TRANSFERASE/RNA / RNA polymerase / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / response to antibiotic / viral RNA genome replication / RNA-dependent RNA polymerase activity / GTPase activity / nucleotide binding / GTP binding / RNA binding ...guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / response to antibiotic / viral RNA genome replication / RNA-dependent RNA polymerase activity / GTPase activity / nucleotide binding / GTP binding / RNA binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) Escherichia phage Qbeta (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.406 Å | ||||||
Authors | Takeshita, D. / Tomita, K. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Molecular basis for RNA polymerization by Q beta replicase 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 | 3avx.cif.gz | 263.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3avx.ent.gz | 204.6 KB | Display | PDB format |
PDBx/mmJSON format | 3avx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3avx_validation.pdf.gz | 818.7 KB | Display | wwPDB validaton report |
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Full document | 3avx_full_validation.pdf.gz | 876.9 KB | Display | |
Data in XML | 3avx_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 3avx_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/3avx ftp://data.pdbj.org/pub/pdb/validation_reports/av/3avx | HTTPS FTP |
-Related structure data
Related structure data | 3avtC 3avuC 3avvC 3avwC 3avyC 3agpS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 141417.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: chimera of Elongation factor Ts, Elongation factor Tu and Q beta replicase Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Escherichia phage Qbeta (virus) Production host: Escherichia coli (E. coli) References: UniProt: P0A6P3, UniProt: P0A6N3, UniProt: Q8LTE0 |
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-RNA chain , 2 types, 2 molecules GT
#2: RNA chain | Mass: 2847.743 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: RNA chain | Mass: 4163.582 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 108 molecules
#4: Chemical | ChemComp-GH3 / | ||
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#5: Chemical | #6: 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: 3.06 Å3/Da / Density % sol: 59.78 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A |
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Detector | Date: Oct 25, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 70424 / Biso Wilson estimate: 41.76 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AGP Resolution: 2.406→19.926 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.7825 / SU ML: 0.35 / σ(F): 1.44 / Phase error: 28.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.03 Å2 / ksol: 0.284 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 155.43 Å2 / Biso mean: 67.6722 Å2 / Biso min: 18.16 Å2
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Refinement step | Cycle: LAST / Resolution: 2.406→19.926 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25
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