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- PDB-1h38: Structure of a T7 RNA polymerase elongation complex at 2.9A resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h38 | ||||||
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Title | Structure of a T7 RNA polymerase elongation complex at 2.9A resolution | ||||||
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![]() | TRANSFERASE / RNA POLYMERASE / T7 RNA POLYMERASE / ELONGATION COMPLEX / PROTEIN/DNA/RNA / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS | ||||||
Function / homology | ![]() DNA-templated viral transcription / mitochondrial promoter sequence-specific DNA binding / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tahirov, T.H. / Temyakov, D. / Anikin, M. / Patlan, V. / McAllister, W.T. / Vassylyev, D.G. / Yokoyama, S. | ||||||
![]() | ![]() Title: Structure of a T7 RNA Polymerase Elongation Complex at 2.9 A Resolution Authors: Tahirov, T.H. / Temiakov, D. / Anikin, M. / Patlan, V. / Mcallister, W.T. / Vassylyev, D.G. / Yokoyama, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 766.7 KB | Display | ![]() |
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PDB format | ![]() | 617.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1qlnS S: Starting model for refinement |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | EACH TETRAMER IS FORMED BY ONE MOLECULE OF PROTEININ COMPLEX WITH 2 MOLECULES OF DNA AND ONE MOLECULEOF RNA. |
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Components
#1: Protein | Mass: 98984.227 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 5526.581 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: RNA chain | Mass: 3851.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: DNA chain | Mass: 2995.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.44 % Description: N-TERMINAL 266 RESIDUES AND ALL PROTRUDING SEGMENTS OF THE C-TERMINAL DOMAIN WERE REMOVED FROM THE SEARCH MODEL | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.1 Details: 10% PEG 8000, 8% GLYCEROL, 5MM BETA-MERCAPTOETHANOL,100 MM TRIS BUFFER, PH8.1, pH 8.10 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 143689 / % possible obs: 94.2 % / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.9 / % possible all: 73.6 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 40 Å / Num. obs: 108303 / % possible obs: 98.1 % / Num. measured all: 348602 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3.08 Å / % possible obs: 94.5 % / Rmerge(I) obs: 0.335 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QLN Resolution: 2.9→39.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3218106.53 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE REMOVED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.0293 Å2 / ksol: 0.334118 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→39.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 40 Å / % reflection Rfree: 4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.9 Å |