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Yorodumi- PDB-4a8y: Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a8y | ||||||
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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/DNA / TRANSFERASE-DNA COMPLEX / VIRAL POLYMERASE / TRANSFERASE | ||||||
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: 3.41 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 | 4a8y.cif.gz | 794.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a8y.ent.gz | 666.9 KB | Display | PDB format |
PDBx/mmJSON format | 4a8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a8y_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4a8y_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4a8y_validation.xml.gz | 66.4 KB | Display | |
Data in CIF | 4a8y_validation.cif.gz | 90 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/4a8y ftp://data.pdbj.org/pub/pdb/validation_reports/a8/4a8y | HTTPS FTP |
-Related structure data
Related structure data | 4a8fC 4a8kC 4a8mC 4a8oC 4a8qC 4a8sC 4a8wC 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: 75033.406 Da / Num. of mol.: 3 / Mutation: YES 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: 4286.789 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: Chemical | #4: Chemical | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 635 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 635 TO GLN ...ENGINEERED | Sequence details | SYNTHETIC SEQUENCE FOR CHAIN F, G, AND H TO FORM A HAIRPIN WITH 4 BASE OVERHANG. THE MET 465 (ILE ...SYNTHETIC SEQUENCE FOR CHAIN F, G, AND H TO FORM A HAIRPIN WITH 4 BASE OVERHANG. 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: 2.74 Å3/Da / Density % sol: 55.08 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.978 |
Detector | Type: ADSC QUANTUM 4 / 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: 3.4→68 Å / Num. obs: 30875 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 67.27 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10 |
-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: 3.41→67.61 Å / Cor.coef. Fo:Fc: 0.8511 / Cor.coef. Fo:Fc free: 0.8091 / Cross valid method: THROUGHOUT / σ(F): 0 Details: NUMBER OF RESTRAINT LIBRARIES USED: 8 REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ATP. NUMBER OF ATOMS WITH PROPER CCP4 ATOM ...Details: NUMBER OF RESTRAINT LIBRARIES USED: 8 REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ATP. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=15826. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=39. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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Displacement parameters | Biso mean: 119.24 Å2
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Refine analyze | Luzzati coordinate error obs: 1.027 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.41→67.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.41→3.53 Å / Total num. of bins used: 15
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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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