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- PDB-6ow3: X-ray crystal structure of a bacterial reiterative transcription ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ow3 | ||||||
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Title | X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter variant -1T | ||||||
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![]() | TRANSCRIPTION/DNA/RNA / RNA polymerase / pyrG / reiterative 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 / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shin, Y. / Murakami, K.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase. Authors: Shin, Y. / Hedglin, M. / Murakami, K.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 727 KB | Display | ![]() |
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PDB format | ![]() | 578.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 547.3 KB | Display | ![]() |
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Full document | ![]() | 623.4 KB | Display | |
Data in XML | ![]() | 119.3 KB | Display | |
Data in CIF | ![]() | 165.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ovrC ![]() 6ovyC ![]() 6oy5C ![]() 6oy6C ![]() 6oy7C ![]() 6p70C ![]() 6p71C ![]() 5vo8S 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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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: 170997.391 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: 6665.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#7: DNA chain | Mass: 8436.442 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: 1495.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 3 types, 5 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/ZN.gif)
#9: Chemical | #10: Chemical | ChemComp-POP / | #11: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.66 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl (pH 8), 0.2M KCl, 50 mM MgCl2, 9.5 % 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: Feb 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→50 Å / Num. obs: 136486 / % possible obs: 97.7 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rpim(I) all: 0.044 / Χ2: 1.108 / Net I/σ(I): 16.24 |
Reflection shell | Resolution: 2.77→2.82 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.29 / Num. unique obs: 5466 / CC1/2: 0.744 / Rpim(I) all: 0.514 / Χ2: 1.119 / % possible all: 78.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VO8 Resolution: 2.766→36.871 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.766→36.871 Å
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Refine LS restraints |
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LS refinement shell |
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