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Yorodumi- PDB-4a8f: Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a8f | ||||||
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Title | Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation | ||||||
Components |
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Keywords | TRANSFERASE / TRANSLATION | ||||||
Function / homology | Function and homology information RNA uridylyltransferase activity / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS PHAGE PHI6 (bacteriophage) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Wright, S. / Poranen, M.M. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M. | ||||||
Citation | Journal: J.Virol. / Year: 2012 Title: Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation. Authors: Wright, S. / Poranen, M.M. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a8f.cif.gz | 787.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a8f.ent.gz | 657.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a8f_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 4a8f_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 4a8f_validation.xml.gz | 71.9 KB | Display | |
Data in CIF | 4a8f_validation.cif.gz | 95.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/4a8f ftp://data.pdbj.org/pub/pdb/validation_reports/a8/4a8f | HTTPS FTP |
-Related structure data
Related structure data | 4a8kC 4a8mC 4a8oC 4a8qC 4a8sC 4a8wC 4a8yC 1hhsS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 75034.398 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS PHAGE PHI6 (bacteriophage) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P11124, RNA-directed RNA polymerase #2: DNA chain | | Mass: 1215.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: Chemical | #4: Chemical | ChemComp-ATP / Sequence details | THE MET 465 (ILE 457) CONFLICT IS OWING TO A SEQUENCE DIFFERENCE (CONFIRMED EXPERIMENTALLY) FROM ...THE MET 465 (ILE 457) CONFLICT IS OWING TO A SEQUENCE DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.43 % / Description: NONE |
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Crystal grow | Details: 20% PEG 4000, 100 MM HEPES (PH 7.5), 8.5% ISOPROPANOL, 15% GLYCEROL, 2 MM MNCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 39855 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 71.66 Å2 / Rmerge(I) obs: 0.27 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 3.3→3.4 Å / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software | Name: BUSTER / Version: 2.9.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHS Resolution: 3.3→46.01 Å / Cor.coef. Fo:Fc: 0.8593 / Cor.coef. Fo:Fc free: 0.8193 / Cross valid method: THROUGHOUT / σ(F): 0 Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ATP. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=15876. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ATP. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=15876. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=168. NUMBER TREATED BY BAD NON- BONDED CONTACTS=4. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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Displacement parameters | Biso mean: 75.22 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→46.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.39 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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