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Yorodumi- PDB-1msw: Structural basis for the transition from initiation to elongation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1msw | ||||||
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Title | Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA/RNA / T7RNAP elongation complex / TRANSCRIPTION-DNA-RNA COMPLEX | ||||||
Function / homology | Function and homology information 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 | Enterobacteria phage T7 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Yin, Y.W. / Steitz, T.A. | ||||||
Citation | Journal: Science / Year: 2002 Title: Structural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase Authors: Yin, Y.W. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1msw.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1msw.ent.gz | 163.9 KB | Display | PDB format |
PDBx/mmJSON format | 1msw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1msw_validation.pdf.gz | 405.9 KB | Display | wwPDB validaton report |
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Full document | 1msw_full_validation.pdf.gz | 468.5 KB | Display | |
Data in XML | 1msw_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 1msw_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/1msw ftp://data.pdbj.org/pub/pdb/validation_reports/ms/1msw | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6117.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Bacteriophage T7 |
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#2: DNA chain | Mass: 5194.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Bacteriophage T7 |
#3: RNA chain | Mass: 3239.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Bacteriophage T7 |
#4: Protein | Mass: 98984.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Plasmid: par1219 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00573, DNA-directed RNA polymerase |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.94 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, LiSO4, Mg(OAc)2, Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 294K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→20 Å / Num. all: 61181 / Num. obs: 61181 / % possible obs: 85 % / Biso Wilson estimate: 24.4 Å2 | |||||||||||||||
Reflection | *PLUS Highest resolution: 2.1 Å / % possible obs: 89.2 % / Rmerge(I) obs: 0.082 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 55.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 4598334.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.6313 Å2 / ksol: 0.299966 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.1 Å2
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Refine analyze | Luzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.77 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.34 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.241 / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.241 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.475 / Rfactor Rwork: 0.482 |