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- PDB-6wox: Thermus thermophilus RNA polymerase initially transcribing comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wox | ||||||
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Title | Thermus thermophilus RNA polymerase initially transcribing complex with 2'dCTP | ||||||
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![]() | TRANSCRIPTION/DNA/RNA / Initially transcribing complex / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex | ||||||
Function / homology | ![]() sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shin, Y. / Murakami, K.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases. Authors: Makinen, J.J. / Shin, Y. / Vieras, E. / Virta, P. / Metsa-Ketela, M. / Murakami, K.S. / Belogurov, G.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 799.8 KB | Display | ![]() |
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PDB format | ![]() | 580.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6woyC ![]() 4q4zS S: Starting model for refinement 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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Unit cell |
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 35056.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase #2: Protein | | Mass: 125436.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 168817.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 11533.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A1J1EUF1, UniProt: Q8RQE7*PLUS, DNA-directed RNA polymerase |
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-DNA chain , 2 types, 2 molecules GH
#6: DNA chain | Mass: 6713.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#7: DNA chain | Mass: 8421.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Protein / RNA chain , 2 types, 2 molecules FI
#5: Protein | Mass: 48598.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#8: RNA chain | Mass: 934.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 4 types, 5 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/DCP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/DCP.gif)
![](data/chem/img/MG.gif)
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#9: Chemical | ChemComp-NA / |
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#10: Chemical | ChemComp-DCP / |
#11: Chemical | ChemComp-MG / |
#12: Chemical |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.59 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl (pH 8), 0.2M KCl, 50 mM MgCl2, 10% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→30 Å / Num. obs: 89931 / % possible obs: 94.3 % / Redundancy: 3.1 % / CC1/2: 0.829 / Rpim(I) all: 0.085 / Χ2: 1.549 / Net I/σ(I): 10.06 |
Reflection shell | Resolution: 3.15→3.2 Å / Mean I/σ(I) obs: 1.44 / Num. unique obs: 3279 / CC1/2: 0.829 / Rpim(I) all: 0.37 / Χ2: 1.152 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Q4Z Resolution: 3.14→29.93 Å / SU ML: 0.4217 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7385
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.14→29.93 Å
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Refine LS restraints |
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LS refinement shell |
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