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Yorodumi- PDB-3t72: PhoB(E)-Sigma70(4)-(RNAP-Betha-flap-tip-helix)-DNA Transcription ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t72 | ||||||
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Title | PhoB(E)-Sigma70(4)-(RNAP-Betha-flap-tip-helix)-DNA Transcription Activation Sub-Complex | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / WINGED-HELIX MOTIF / TRANSCRIPTION ACTIVATION / DNA-BINDING / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information bacterial-type RNA polymerase holo enzyme binding / phosphate ion transport / sigma factor antagonist complex / phosphorelay response regulator activity / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / protein-DNA complex / response to heat ...bacterial-type RNA polymerase holo enzyme binding / phosphate ion transport / sigma factor antagonist complex / phosphorelay response regulator activity / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / protein-DNA complex / response to heat / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4.33 Å | ||||||
Authors | Blanco, A.G. / Canals, A. / Bernues, J. / Sola, M. / Coll, M. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: The structure of a transcription activation subcomplex reveals how sigma (70) is recruited to PhoB promoters. Authors: Blanco, A.G. / Canals, A. / Bernues, J. / Sola, M. / Coll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t72.cif.gz | 407.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t72.ent.gz | 307.9 KB | Display | PDB format |
PDBx/mmJSON format | 3t72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t72_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
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Full document | 3t72_full_validation.pdf.gz | 527.4 KB | Display | |
Data in XML | 3t72_validation.xml.gz | 22 KB | Display | |
Data in CIF | 3t72_validation.cif.gz | 59.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/3t72 ftp://data.pdbj.org/pub/pdb/validation_reports/t7/3t72 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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12 |
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Unit cell |
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Details | The biological assembly is that formed by chains A,B,C,D,q and r |
-Components
#1: Protein | Mass: 11971.624 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: phoB, b0399, JW0389 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFJ5 #2: DNA chain | Mass: 8035.216 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: Synthesized DNA / Source: (synth.) Escherichia coli (E. coli) #3: DNA chain | Mass: 7937.140 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: Synthesized DNA / Source: (synth.) Escherichia coli (E. coli) #4: Protein | Mass: 11080.619 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoD, alt, b3067, JW3039, EKO11_4334, rpoB / Production host: Escherichia coli (E. coli) References: UniProt: P00579, UniProt: E8Y6A0, DNA-directed RNA polymerase |
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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: 5.81 Å3/Da / Density % sol: 78.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 8-10% PEG 4000, 100 mM KCl, 10 mM magnesium chloride, 50 mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2542,1.2554,1.2498 | ||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 27, 2006 | ||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 4.33→50 Å / Num. all: 73615 / Num. obs: 73615 / % possible obs: 100 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 4.33→50 Å / Num. reflection obs: 73615 Details: CLOSE CONTACTS OF DNA ATOMS WITH SYMMETRY-EQUIVALENT NEIGHBOUR DNA MOLECULES FORMING PSEUDO-CONTINUOUS HELICES ARE DUE TO LACK OF ATOMIC POSITIONAL REFINEMENT | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.33→50 Å
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