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- PDB-4a8m: Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a8m | ||||||
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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 | ||||||
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![]() | TRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / VIRAL POLYMERASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wright, S. / Poranen, M.M. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 781.3 KB | Display | ![]() |
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PDB format | ![]() | 649.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 67.7 KB | Display | |
Data in CIF | ![]() | 91.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a8fC ![]() 4a8kC ![]() 4a8oC ![]() 4a8qC ![]() 4a8sC ![]() 4a8wC ![]() 4a8yC 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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3 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 1174.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||||
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#2: Protein | Mass: 75034.398 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Chemical | Sequence details | DNA SYNTHETIC SEQUENCE TO FORM A HAIRPIN WITH A 2 BASE OVERHANG. THE MET 465 (ILE 457) CONFLICT IS ...DNA SYNTHETIC SEQUENCE TO FORM A HAIRPIN WITH A 2 BASE OVERHANG. THE MET 465 (ILE 457) CONFLICT IS OWING TO A SEQUENCE DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.8 % / 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: ![]() ![]() ![]() |
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: 2.9→59 Å / Num. obs: 55288 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 81.12 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.92→3 Å |
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Processing
Software | Name: BUSTER / Version: 2.9.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.92→58.72 Å / Cor.coef. Fo:Fc: 0.8944 / Cor.coef. Fo:Fc free: 0.8728 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY.
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Displacement parameters | Biso mean: 66.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.377 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.92→58.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.92→3 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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