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Yorodumi- PDB-2o5j: Crystal structure of the T. thermophilus RNAP polymerase elongati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o5j | ||||||
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Title | Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the NTP substrate analog | ||||||
Components |
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Keywords | TRANSFERASE/DNA-RNA HYBRID / RNA polymerase / elongation complex / template DNA / non-template DNA / RNA transcript / NTP substrate / TRANSFERASE-DNA-RNA HYBRID COMPLEX | ||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / 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 / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Vassylyev, D.G. / Vassylyeva, M.N. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Structural basis for substrate loading in bacterial RNA polymerase. Authors: Vassylyev, D.G. / Vassylyeva, M.N. / Zhang, J. / Palangat, M. / Artsimovitch, I. / Landick, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o5j.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2o5j.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 2o5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o5j_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2o5j_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2o5j_validation.xml.gz | 306.5 KB | Display | |
Data in CIF | 2o5j_validation.cif.gz | 430.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/2o5j ftp://data.pdbj.org/pub/pdb/validation_reports/o5/2o5j | HTTPS FTP |
-Related structure data
Related structure data | 2ppbC 2o5iS 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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Details | The asymmetric unit contains the two molecules of the complex. The biological assembly is a monomeric complex. |
-Components
-DNA chain , 2 types, 4 molecules GXIZ
#1: DNA chain | Mass: 7001.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA template strand #3: DNA chain | Mass: 4323.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA non-template strand |
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-RNA chain , 1 types, 2 molecules HY
#2: RNA chain | Mass: 5184.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA transcript |
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-DNA-directed RNA polymerase ... , 4 types, 10 molecules ABKLCMDNEO
#4: 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 #5: 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 #6: 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 #7: 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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-Non-polymers , 4 types, 2643 molecules
#8: Chemical | ChemComp-ZN / #9: Chemical | ChemComp-MG / #10: Chemical | #11: 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: 3.85 Å3/Da / Density % sol: 68.05 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% MPD, 0.1M Na cacodylate, 0.2M Mg acetate, 2mM AMPcPP, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 25, 2006 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. all: 236997 / Num. obs: 211633 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.1 / Num. unique all: 17916 / Rsym value: 0.441 / % possible all: 75.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2O5I Resolution: 3→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 63.1 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å
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