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- PDB-6p70: X-ray crystal structure of bacterial RNA polymerase and pyrBI pro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6p70 | ||||||
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Title | X-ray crystal structure of bacterial RNA polymerase and pyrBI promoter complex | ||||||
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![]() | TRANSCRIPTION/DNA / RNA polymerase / pyrBI / reiterative transcription / TRANSCRIPTION / TRANSCRIPTION-DNA 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 | ![]() | 723.7 KB | Display | ![]() |
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PDB format | ![]() | 578.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ovrC ![]() 6ovyC ![]() 6ow3C ![]() 6oy5C ![]() 6oy6C ![]() 6oy7C ![]() 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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-Protein , 1 types, 1 molecules F
#5: Protein | Mass: 48598.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-DNA chain , 2 types, 2 molecules GH
#6: DNA chain | Mass: 6360.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#7: DNA chain | Mass: 8362.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 2 types, 5 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#8: Chemical | #9: Chemical | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.09 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 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: May 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: 3.05→50 Å / Num. obs: 101835 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rpim(I) all: 0.068 / Χ2: 1.099 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 3.05→3.13 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.21 / Num. unique obs: 4930 / CC1/2: 0.73 / Rpim(I) all: 0.549 / Χ2: 0.73 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VO8 Resolution: 3.052→46.061 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.96 / 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: 3.052→46.061 Å
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Refine LS restraints |
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LS refinement shell |
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