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Yorodumi- PDB-1h38: Structure of a T7 RNA polymerase elongation complex at 2.9A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h38 | ||||||
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Title | Structure of a T7 RNA polymerase elongation complex at 2.9A resolution | ||||||
Components |
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Keywords | TRANSFERASE / RNA POLYMERASE / T7 RNA POLYMERASE / ELONGATION COMPLEX / PROTEIN/DNA/RNA / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information DNA-templated viral transcription / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | BACTERIOPHAGE T7 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Tahirov, T.H. / Temyakov, D. / Anikin, M. / Patlan, V. / McAllister, W.T. / Vassylyev, D.G. / Yokoyama, S. | ||||||
Citation | Journal: Nature / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h38.cif.gz | 766.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h38.ent.gz | 617.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h38_validation.pdf.gz | 507.7 KB | Display | wwPDB validaton report |
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Full document | 1h38_full_validation.pdf.gz | 775.9 KB | Display | |
Data in XML | 1h38_validation.xml.gz | 106.5 KB | Display | |
Data in CIF | 1h38_validation.cif.gz | 159.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/1h38 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/1h38 | HTTPS FTP |
-Related structure data
Related structure data | 1qlnS S: Starting model for refinement |
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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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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. |
-Components
#1: Protein | Mass: 98984.227 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTERIOPHAGE T7 (virus) / Plasmid: PAR1219 / Cell line (production host): DCAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00573, DNA-directed RNA polymerase #2: DNA chain | Mass: 5526.581 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE T7 (virus) #3: RNA chain | Mass: 3851.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE T7 (virus) #4: DNA chain | Mass: 2995.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE T7 (virus) #5: 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: 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |