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Yorodumi- PDB-1tkd: T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tkd | ||||||
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Title | T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site | ||||||
Components |
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Keywords | TRANSFERASE/ELECTRON TRANSPORT/DNA / 8-oxoguanosine DNA polymerase / TRANSFERASE-ELECTRON TRANSPORT-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA synthesis involved in DNA replication / DNA exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / double-strand break repair via alternative nonhomologous end joining / DNA polymerase processivity factor activity / protein-disulfide reductase activity / 3'-5' exonuclease activity / cell redox homeostasis / DNA-templated DNA replication ...DNA synthesis involved in DNA replication / DNA exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / double-strand break repair via alternative nonhomologous end joining / DNA polymerase processivity factor activity / protein-disulfide reductase activity / 3'-5' exonuclease activity / cell redox homeostasis / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Enterobacteria phage T7 (virus) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Brieba, L.G. / Eichman, B.F. / Kokoska, R.J. / Doublie, S. / Kunkel, T.A. / Ellenberger, T. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. Authors: Brieba, L.G. / Eichman, B.F. / Kokoska, R.J. / Doublie, S. / Kunkel, T.A. / Ellenberger, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tkd.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tkd.ent.gz | 164.2 KB | Display | PDB format |
PDBx/mmJSON format | 1tkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tkd_validation.pdf.gz | 823.3 KB | Display | wwPDB validaton report |
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Full document | 1tkd_full_validation.pdf.gz | 843.6 KB | Display | |
Data in XML | 1tkd_validation.xml.gz | 41.5 KB | Display | |
Data in CIF | 1tkd_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/1tkd ftp://data.pdbj.org/pub/pdb/validation_reports/tk/1tkd | HTTPS FTP |
-Related structure data
Related structure data | 1t8eC 1tk0C 1tk5C 1tk8C 1t7pS C: citing same article (ref.) 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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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules PT
#1: DNA chain | Mass: 6724.373 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 7963.088 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 2 types, 2 molecules AB
#3: Protein | Mass: 79089.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: 5 / Plasmid: pGP5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00581, DNA-directed DNA polymerase |
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#4: Protein | Mass: 11687.388 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: TRXA, TSNC, FIPA, B3781, C4701, Z5291, ECS4714, STM3915, STMD1.75, STY3639, T3381, SF3854, S3905 Plasmid: pTrx-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0AA25 |
-Non-polymers , 6 types, 725 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-D3T / | #8: Chemical | ChemComp-MES / | #9: Chemical | ChemComp-1PE / | #10: 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 Å3/Da / Density % sol: 58.3 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG8000, Ammonium Sulfate, PEG400, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2004 / Details: mirrors |
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: 2.49→50 Å / Num. obs: 40910 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Biso Wilson estimate: 28.6 Å2 / Rsym value: 0.071 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.48→2.57 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 8.4 / Num. unique all: 40910 / Rsym value: 0.253 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T7P Resolution: 2.49→47.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1977204.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7709 Å2 / ksol: 0.327916 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.49→47.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.64 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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