+Open data
-Basic information
Entry | Database: PDB / ID: 3aoi | ||||||
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Title | RNA polymerase-Gfh1 complex (Crystal type 2) | ||||||
Components |
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Keywords | Transcription / TRANSFERASE/DNA/RNA / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / TRANSFERASE-DNA-RNA complex | ||||||
Function / homology | Function and homology information RNA polymerase binding / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...RNA polymerase binding / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / 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: 4.3 Å | ||||||
Authors | Tagami, S. / Sekine, S. / Kumarevel, T. / Yamamoto, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Nature / Year: 2010 Title: Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein Authors: Tagami, S. / Sekine, S.I. / Kumarevel, T. / Hino, N. / Murayama, Y. / Kamegamori, S. / Yamamoto, M. / Sakamoto, K. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aoi.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3aoi.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 3aoi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/3aoi ftp://data.pdbj.org/pub/pdb/validation_reports/ao/3aoi | HTTPS FTP |
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-Related structure data
Related structure data | 3aohSC 2f23S 2o5iS 3dxjS 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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3 |
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Unit cell |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 15 molecules ABFGKLCHMDINEJO
#1: Protein | Mass: 35056.164 Da / Num. of mol.: 6 / 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.: 3 / 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.: 3 / 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.: 3 / 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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-DNA chain / RNA chain / Protein , 3 types, 9 molecules PRTQSUXYZ
#5: DNA chain | Mass: 8238.298 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: DNA oligomer #6: RNA chain | Mass: 10366.212 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: RNA oligomer #7: Protein | Mass: 17206.482 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1042 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJG6 |
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-Non-polymers , 2 types, 6 molecules
#8: Chemical | #9: Chemical | |
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-Details
Sequence details | ONE MORE DNA OLIGOMER (NONTEMPLATE DNA) WAS USED IN CRYSTALLIZATION, HOWEVER ITS ELECTRON DENSITY ...ONE MORE DNA OLIGOMER (NONTEMPLAT |
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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: 3.49 Å3/Da / Density % sol: 64.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 50mM Hepes-NaOH buffer (pH 6.4), 5.5% PEG 8000, 300mM LiCl, 10mM MgCl2, 1% dimethyl sulfoxide, 5mM taurine, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9801 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 4.3→50 Å / Num. obs: 112834 / % possible obs: 97.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2O5I, 3DXJ, 2F23, and 3AOH Resolution: 4.3→47.57 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 8706429.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 102.644 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 160.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 4.3→47.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.3→4.57 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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