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Yorodumi- PDB-4oir: Crystal structure of Thermus thermophilus RNA polymerase transcri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oir | ||||||
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Title | Crystal structure of Thermus thermophilus RNA polymerase transcription initiation complex soaked with GE23077 and rifamycin SV | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSFERASE/ANTIBIOTIC / GE23077 / transcription inhibitor / transcription open complex / transcription initiation complex / rifamycin SV / i site / i+1 site / RNA polymerase / DNA/RNA/NTP binding / polymerization of ribonucleotides / nucleoid / TRANSFERASE-ANTIBIOTIC 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) Actinomadura sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.105 Å | ||||||
Authors | Zhang, Y. / Ebright, R.H. / Arnold, E. | ||||||
Citation | Journal: Elife / Year: 2014 Title: GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides. Authors: Zhang, Y. / Degen, D. / Ho, M.X. / Sineva, E. / Ebright, K.Y. / Ebright, Y.W. / Mekler, V. / Vahedian-Movahed, H. / Feng, Y. / Yin, R. / Tuske, S. / Irschik, H. / Jansen, R. / Maffioli, S. / ...Authors: Zhang, Y. / Degen, D. / Ho, M.X. / Sineva, E. / Ebright, K.Y. / Ebright, Y.W. / Mekler, V. / Vahedian-Movahed, H. / Feng, Y. / Yin, R. / Tuske, S. / Irschik, H. / Jansen, R. / Maffioli, S. / Donadio, S. / Arnold, E. / Ebright, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oir.cif.gz | 738.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oir.ent.gz | 585.1 KB | Display | PDB format |
PDBx/mmJSON format | 4oir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oir_validation.pdf.gz | 991.1 KB | Display | wwPDB validaton report |
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Full document | 4oir_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4oir_validation.xml.gz | 118.3 KB | Display | |
Data in CIF | 4oir_validation.cif.gz | 160.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/4oir ftp://data.pdbj.org/pub/pdb/validation_reports/oi/4oir | HTTPS FTP |
-Related structure data
Related structure data | 4mq9C 4oinC 4oioC 4oipC 4oiqC 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: 33878.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / 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 (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 (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 (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 / Details: promoter DNA template strand |
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#7: DNA chain | Mass: 8421.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: promoter DNA nontemplate strand |
-Protein / Protein/peptide , 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 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: rpoD, TTHA0532 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKW1 |
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#8: Protein/peptide | |
-Non-polymers , 5 types, 131 molecules
#9: Chemical | ChemComp-MG / #10: Chemical | ChemComp-RFV / | #11: Chemical | #12: Chemical | ChemComp-MB8 / ( | #13: 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: 3.19 Å3/Da / Density % sol: 61.43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 100 mM Tris-HCl, pH 8.4, 200 mM potassium chloride, 50 mM magnesium chloride, 9.5% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 101511 / Num. obs: 98567 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 63.48 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.3 / Num. unique all: 3894 / Rsym value: 0.727 / % possible all: 77.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4G7H Resolution: 3.105→47.496 Å / SU ML: 0.41 / Isotropic thermal model: ISOTROPIC / σ(F): 1.33 / Phase error: 27.31 / 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 mean: 59.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.105→47.496 Å
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Refine LS restraints |
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LS refinement shell |
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