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Open data
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Basic information
| Entry | Database: PDB / ID: 5ipm | ||||||
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| Title | SigmaS-transcription initiation complex with 4-nt nascent RNA | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSFERASE/DNA/RNA / Transcription initiation / RNA polymerase / general stress sigma factor / pyrophosphate release / TRANSFERASE-DNA-RNA complex | ||||||
| Function / homology | Function and homology informationsigma factor antagonist complex / RNA polymerase complex / response to stress / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex ...sigma factor antagonist complex / RNA polymerase complex / response to stress / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
| Biological species | ![]() synthetic construct (others) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | ||||||
Authors | Liu, B. / Zuo, Y. / Steitz, T.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016Title: Structures of E. coli sigma S-transcription initiation complexes provide new insights into polymerase mechanism. Authors: Liu, B. / Zuo, Y. / Steitz, T.A. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5ipm.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb5ipm.ent.gz | 1.2 MB | Display | PDB format |
| PDBx/mmJSON format | 5ipm.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5ipm_validation.pdf.gz | 512.5 KB | Display | wwPDB validaton report |
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| Full document | 5ipm_full_validation.pdf.gz | 599.3 KB | Display | |
| Data in XML | 5ipm_validation.xml.gz | 137.9 KB | Display | |
| Data in CIF | 5ipm_validation.cif.gz | 182.9 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/5ipm ftp://data.pdbj.org/pub/pdb/validation_reports/ip/5ipm | HTTPS FTP |
-Related 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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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 6 - 232 / Label seq-ID: 13 - 239
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
| #1: Protein | Mass: 26899.572 Da / Num. of mol.: 2 / Fragment: UNP residues 1-235 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | | Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Production host: ![]() #3: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | | Mass: 10118.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-DNA chain , 2 types, 2 molecules 12
| #6: DNA chain | Mass: 15329.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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| #7: DNA chain | Mass: 15547.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / RNA chain , 2 types, 2 molecules F3
| #5: Protein | Mass: 38777.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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| #8: RNA chain | Mass: 1440.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 3 molecules 


| #9: Chemical | | #10: Chemical | ChemComp-MG / | |
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-Details
| Has protein modification | Y |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.82 % |
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| Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: PEG3350, sodium chloride, HEPES |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
| Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2014 |
| Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
| Reflection | Resolution: 4.2→126.464 Å / Num. obs: 32692 / % possible obs: 99.9 % / Redundancy: 7.7 % / Net I/σ(I): 8.44 |
| Reflection shell | Highest resolution: 4.2 Å |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→126.46 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.889 / SU B: 371.28 / SU ML: 1.82 / Cross valid method: THROUGHOUT / ESU R Free: 1.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 284.432 Å2
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| Refinement step | Cycle: LAST / Resolution: 4.2→126.46 Å
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| Refine LS restraints |
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