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Yorodumi- PDB-4g7z: Crystal structure of Thermus thermophilus transcription initiatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g7z | ||||||
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Title | Crystal structure of Thermus thermophilus transcription initiation complex containing 5-BrU at template-strand position +1 | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSFERASE/DNA / protein-DNA complex / transcription initiation complex / RNAP-promoter complex / RNAP-promoter open complex / open complex / RPo / RNA polymerase / transcription initiation / transcription Initiation factor sigma A / promoter DNA / nucleoid / 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 | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.815 Å | ||||||
Authors | Zhang, Y. / Ebright, R.H. | ||||||
Citation | Journal: Science / Year: 2012 Title: Structural basis of transcription initiation. Authors: Zhang, Y. / Feng, Y. / Chatterjee, S. / Tuske, S. / Ho, M.X. / 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 | 4g7z.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4g7z.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 4g7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/4g7z ftp://data.pdbj.org/pub/pdb/validation_reports/g7/4g7z | HTTPS FTP |
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-Related structure data
Related structure data | 4g7hSC 4g7oC 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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2 |
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Unit cell |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABKLCMDNEO
#1: Protein | Mass: 35056.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHR6, DNA-directed RNA polymerase #2: Protein | Mass: 125436.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q8RQE9, DNA-directed RNA polymerase #3: Protein | Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q8RQE8, DNA-directed RNA polymerase #4: Protein | Mass: 11533.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q8RQE7, DNA-directed RNA polymerase |
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-Protein , 1 types, 2 molecules FP
#5: Protein | Mass: 50769.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpoD, TTHA0532 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKW1 |
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-DNA chain , 2 types, 4 molecules HRGQ
#6: DNA chain | Mass: 8421.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: nontemplate strand #7: DNA chain | Mass: 6545.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: template strand |
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-Non-polymers , 2 types, 6 molecules
#8: Chemical | ChemComp-ZN / #9: Chemical | |
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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: 3.18 Å3/Da / Density % sol: 61.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 100 mM Tris-HCl, pH 8.7, 200 mM potassium chloride, 50 mM magnesium chloride, 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 4, 2011 |
Radiation | Monochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. all: 109211 / Num. obs: 97590 / % possible obs: 89.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.174 / Rsym value: 0.174 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3.8→3.87 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.553 / % possible all: 46.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4G7H Resolution: 3.815→49.846 Å / SU ML: 0.46 / σ(F): 0 / Phase error: 26.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 109.109 Å2 / ksol: 0.302 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.815→49.846 Å
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Refine LS restraints |
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LS refinement shell |
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