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Yorodumi- PDB-6lts: Crystal structure of Thermus thermophilus transcription initiatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lts | ||||||
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Title | Crystal structure of Thermus thermophilus transcription initiation complex comprising a truncated sigma finger | ||||||
Components |
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Keywords | TRANSCRIPTION / sigma factor / bacterial transcription / transcription initiation / RNA polymerase / initiation factor / sigma finger | ||||||
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 | Thermus thermophilus HB8 (bacteria) Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å | ||||||
Authors | Zhang, Y. / Ebright, R.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. Authors: Li, L. / Molodtsov, V. / Lin, W. / Ebright, R.H. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lts.cif.gz | 783.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lts.ent.gz | 573.1 KB | Display | PDB format |
PDBx/mmJSON format | 6lts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/6lts ftp://data.pdbj.org/pub/pdb/validation_reports/lt/6lts | HTTPS FTP |
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-Related structure data
Related structure data | 6konC 6kooC 6kopC 6koqC 6kqdC 6kqeC 6kqfC 6kqgC 6kqhC 6kqlC 6kqmC 6kqnC 6l74C 6tyeC 6tyfC 6tygC 4g7hS 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: 35056.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q5SHR6, DNA-directed RNA polymerase #2: Protein | | Mass: 125436.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q8RQE9, DNA-directed RNA polymerase #3: Protein | | Mass: 170997.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q8RQE8, DNA-directed RNA polymerase #4: Protein | | Mass: 11533.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / References: UniProt: Q8RQE7, DNA-directed RNA polymerase |
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-Protein , 1 types, 1 molecules F
#5: Protein | Mass: 50769.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: sigA, TTHA0532 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKW1 |
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-DNA chain , 2 types, 2 molecules HG
#6: DNA chain | Mass: 8421.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) |
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#7: DNA chain | Mass: 5821.760 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) |
-Non-polymers , 2 types, 7 molecules
#8: Chemical | ChemComp-MG / #9: Chemical | |
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-Details
Has ligand of interest | N |
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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: 3.15 Å3/Da / Density % sol: 60.95 % / Description: rod-like |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 8.7 Details: 100 mM Tris-HCl, pH 8.7, 200 mM potassium chloride, 50 mM magnesium chloride, 10% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Oct 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→45 Å / Num. obs: 72642 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 81.76 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/av σ(I): 1.043 / Net I/σ(I): 8.514 |
Reflection shell | Resolution: 3.45→3.51 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.757 / Num. unique obs: 3627 / Rsym value: 0.695 / Χ2: 0.904 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G7H Resolution: 3.45→44.23 Å / SU ML: 0.4755 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.607
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 101.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.45→44.23 Å
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Refine LS restraints |
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LS refinement shell |
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