+Open data
-Basic information
Entry | Database: PDB / ID: 6dta | |||||||||
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Title | Bacteriophage N4 RNA polymerase II elongation complex 2 | |||||||||
Components |
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Keywords | transcription/dna/rna / Bacteriophage / N4 / RNA polymerase / TRANSCRIPTION / transcription-dna-rna complex | |||||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | Enterobacteria phage N4 (virus) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.694 Å | |||||||||
Authors | Molodtsov, V. / Murakami, K.S. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II. Authors: Molodtsov, V. / Murakami, K.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dta.cif.gz | 307.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dta.ent.gz | 246.3 KB | Display | PDB format |
PDBx/mmJSON format | 6dta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/6dta ftp://data.pdbj.org/pub/pdb/validation_reports/dt/6dta | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31604.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage N4 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTE4 |
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#2: Protein | Mass: 46381.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage N4 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTE3 |
-DNA chain / RNA chain , 2 types, 2 molecules CD
#3: DNA chain | Mass: 14648.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: RNA chain | Mass: 2560.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 18 molecules
#5: Chemical | ChemComp-GTP / | ||
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#6: Chemical | #7: 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: 3.08 Å3/Da / Density % sol: 60.09 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion Details: 0.17 M sodium acetate, 0.085 M sodium cacodylate (pH 6.5), 15% PEG8000, 15% glycerol and 5 microM spermine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9782 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9782 Å / Relative weight: 1 |
Reflection | Resolution: 2.6939→29.923 Å / Num. obs: 31537 / % possible obs: 97.91 % / Redundancy: 4.5 % / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 2.6939→2.7613 Å |
-Processing
Software |
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Refinement | Resolution: 2.694→29.923 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.694→29.923 Å
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Refine LS restraints |
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LS refinement shell |
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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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