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Yorodumi- PDB-6n62: Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstr... -
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-Basic information
Entry | Database: PDB / ID: 6n62 | ||||||
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Title | Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Complex / RNA polymerase / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.803 Å | ||||||
Authors | Braffman, N. / Hauver, J. / Campbell, E.A. / Darst, S.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Authors: Braffman, N.R. / Piscotta, F.J. / Hauver, J. / Campbell, E.A. / Link, A.J. / Darst, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n62.cif.gz | 738.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n62.ent.gz | 580.7 KB | Display | PDB format |
PDBx/mmJSON format | 6n62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n62_validation.pdf.gz | 522.7 KB | Display | wwPDB validaton report |
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Full document | 6n62_full_validation.pdf.gz | 635.8 KB | Display | |
Data in XML | 6n62_validation.xml.gz | 127.9 KB | Display | |
Data in CIF | 6n62_validation.cif.gz | 170.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/6n62 ftp://data.pdbj.org/pub/pdb/validation_reports/n6/6n62 | HTTPS FTP |
-Related structure data
Related structure data | 6n60C 6n61C 4ljzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 26459.125 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-234) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, Z4665, ECs4160 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A7Z6, DNA-directed RNA polymerase #2: Protein | | Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB, Z5560, ECs4910 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8V4, DNA-directed RNA polymerase #3: Protein | | Mass: 155576.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, Z5561, ECs4911 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8T8, DNA-directed RNA polymerase #4: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, Z5075, ECs4524 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A802, DNA-directed RNA polymerase |
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-Protein , 1 types, 1 molecules F
#5: Protein | Mass: 70351.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0P6L9 |
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-DNA chain , 2 types, 2 molecules NT
#6: DNA chain | Mass: 8924.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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#7: DNA chain | Mass: 7363.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-Non-polymers , 2 types, 3 molecules
#8: Chemical | ChemComp-MG / |
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#9: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.76 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1 M HEPES, pH 6.8, 0.2 M magnesium chloride, 7% w/v PEG3350, 4% v/v glycerol, 4% v/v ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9198 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 10, 2015 |
Radiation | Monochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 59257 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 1 / Rpim(I) all: 0.032 / Net I/σ(I): 12.34 |
Reflection shell | Resolution: 3.8→3.94 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 0.59 / Num. unique obs: 5662 / CC1/2: 0.355 / Rpim(I) all: 1.554 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4LJZ Resolution: 3.803→24.883 Å / SU ML: 0.73 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.09 / 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: 3.803→24.883 Å
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Refine LS restraints |
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LS refinement shell |
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