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- PDB-2ppb: Crystal structure of the T. thermophilus RNAP polymerase elongati... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ppb | ||||||
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Title | Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin | ||||||
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![]() | TRANSFERASE/DNA/RNA / RNA POLYMERASE / ELONGATION COMPLEX / TEMPLATE DNA / NON-TEMPLATE DNA / RNA TRANSCRIPT / NTP SUBSTRATE / ANTIBIOTIC STREPTOLYDIGIN / TRANSFERASE-DNA-RNA COMPLEX | ||||||
Function / homology | ![]() DNA-directed RNA polymerase complex / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity ...DNA-directed RNA polymerase complex / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vassylyev, D.G. / Vassylyeva, M.N. / Artsimovitch, I. / Landick, R. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 307.5 KB | Display | |
Data in CIF | ![]() | 430.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2o5jC ![]() 2o5iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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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) ![]() ![]() References: UniProt: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase #5: Protein | Mass: 125436.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 11533.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 2482 molecules 








#8: Chemical | #9: Chemical | ChemComp-ZN / #10: Chemical | ChemComp-MG / #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.05 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% MPD, 0.1M NA CACODYLATE, 0.2M MG ACETATE, 2MM AMPCPP, 2MM STD, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 6.50, temperature 295K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 207148 / Num. obs: 207148 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.2 / Num. unique all: 16469 / Rsym value: 0.439 / % possible all: 70.1 |
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Processing
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Refinement | Method to determine structure: ![]() 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 Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED ...Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED OUT USING THE TWINNING OPTION OF THE CNS PROGRAM. FOR THE DEPOSITION THE DIFFRACTION DATA WERE DETWINNED USING THE CNS PROGRAM. THEREFORE, SOME REFLECTIONS WERE LOST DUE TO THE DETWINNING PROCEDURE AND ARE MISSING IN THE DEPOSITED SF FILE, WHEREAS THE REFINEMENT STATISTICS CALCULATED BASED ON THE DETWINNED ATA MIGHT BE SLIGHTLY DIFFERENT FROM THOSE OBTAINED DURING THE "TWINNED" REFINEMENT INCLUDED IN THIS ENTRY.
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Displacement parameters | Biso mean: 55.1 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 / Total num. of bins used: 10
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