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Yorodumi- PDB-5e17: T. thermophilus transcription initiation complex having a RRR dis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+17 | ||||||
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Title | T. thermophilus transcription initiation complex having a RRR discriminator sequence and a nontemplate-strand length corresponding to TSS selection at position 7 (RPo-GGG-7) | ||||||
Components |
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Keywords | transcription/dna/rna / DNA / Single-Stranded / DNA-Directed RNA Polymerases / Gene Expression Regulation / Bacterial / Promoter Regions / Protein Conformation / Sigma Factor / Thermus thermophilus / Transcription Initiation / start site selection / promoter escape / initial transcript / abortive product / sigma finger / transcription-dna-rna 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 | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Zhang, Y. / Ebright, R.H. | ||||||
Citation | Journal: Science / Year: 2016 Title: Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Authors: Winkelman, J.T. / Vvedenskaya, I.O. / Zhang, Y. / Zhang, Y. / Bird, J.G. / Taylor, D.M. / Gourse, R.L. / Ebright, R.H. / Nickels, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e17.cif.gz | 742.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e17.ent.gz | 585.6 KB | Display | PDB format |
PDBx/mmJSON format | 5e17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e17_validation.pdf.gz | 523.9 KB | Display | wwPDB validaton report |
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Full document | 5e17_full_validation.pdf.gz | 570.9 KB | Display | |
Data in XML | 5e17_validation.xml.gz | 118.5 KB | Display | |
Data in CIF | 5e17_validation.cif.gz | 163.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/5e17 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/5e17 | HTTPS FTP |
-Related structure data
Related structure data | 5e18C 4g7hS C: citing same article (ref.) S: Starting model for refinement |
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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 (bacteria) 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) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE7, DNA-directed RNA polymerase |
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-DNA chain , 2 types, 2 molecules GH
#6: DNA chain | Mass: 6480.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) |
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#7: DNA chain | Mass: 8421.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) |
-Protein / RNA chain , 2 types, 2 molecules FI
#5: Protein | Mass: 50769.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: sigA, TTHA0532 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKW1 |
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#8: RNA chain | Mass: 2156.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA -6+1 / Source: (synth.) Thermus thermophilus (bacteria) |
-Non-polymers , 3 types, 165 molecules
#9: Chemical | ChemComp-MG / #10: Chemical | #11: Water | ChemComp-HOH / | |
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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: 3.09 Å3/Da / Density % sol: 60.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris-HCl, pH 8.4, 200 mM potassium chloride, 50 mM magnesium chloride, 9.5% PEG4000, |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→40 Å / Num. obs: 85564 / % possible obs: 93.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 61.3 Å2 / Rmerge(I) obs: 0.185 / Χ2: 1.029 / Net I/av σ(I): 6.519 / Net I/σ(I): 4.3 / Num. measured all: 297050 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G7H Resolution: 3.2→39.817 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.78 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 185.5 Å2 / Biso mean: 62.3206 Å2 / Biso min: 6.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→39.817 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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