+Open data
-Basic information
Entry | Database: PDB / ID: 3aoh | ||||||
---|---|---|---|---|---|---|---|
Title | RNA polymerase-Gfh1 complex (Crystal type 1) | ||||||
Components |
| ||||||
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: 4.1 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3aoh.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3aoh.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 3aoh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/3aoh ftp://data.pdbj.org/pub/pdb/validation_reports/ao/3aoh | HTTPS FTP |
---|
-Related structure data
Related structure data | 3aoiC 2f23S 2o5iS 3dxjS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-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 |
---|
-DNA chain / RNA chain / Protein , 3 types, 5 molecules PQXYZ
#5: DNA chain | Mass: 8238.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligomer |
---|---|
#6: RNA chain | Mass: 10671.394 Da / Num. of mol.: 1 / 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 |
-Non-polymers , 2 types, 6 molecules
#8: Chemical | #9: Chemical | |
---|
-Details
Sequence details | ONE MORE DNA OLIGOMER (NONTEMPLATE DNA) WAS USED IN CRYSTALLIZATION, HOWEVER ITS ELECTRON DENSITY ...ONE MORE DNA OLIGOMER (NONTEMPLAT |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.49 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9801 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 25, 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: 4.1→50 Å / Num. obs: 131790 / % possible obs: 96.8 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2O5I, 3DXJ, and 2F23 Resolution: 4.1→49.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 8802719.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 108.99 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 171.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.1→49.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 4.1→4.36 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|