+Open data
-Basic information
Entry | Database: PDB / ID: 1skr | ||||||
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Title | T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP | ||||||
Components |
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Keywords | TRANSFERASE/ELECTRON TRANSPORT/DNA / DNA polymerase / uv-lesion / replication / open / close / 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 / 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 synthesis involved in DNA replication / DNA exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Enterobacteria phage T7 (virus) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Li, Y. / Dutta, S. / Doublie, S. / Bdour, H.M. / Taylor, J.S. / Ellenberger, T. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7. Authors: Li, Y. / Dutta, S. / Doublie, S. / Bdour, H.M. / Taylor, J.S. / Ellenberger, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1skr.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1skr.ent.gz | 145.6 KB | Display | PDB format |
PDBx/mmJSON format | 1skr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/1skr ftp://data.pdbj.org/pub/pdb/validation_reports/sk/1skr | HTTPS FTP |
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-Related 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: 6748.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer |
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#2: DNA chain | Mass: 7913.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template |
-Protein , 2 types, 2 molecules AB
#3: Protein | Mass: 79089.789 Da / Num. of mol.: 1 / Mutation: DEL(118-123) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: 5 / Production host: Escherichia coli (E. coli) / 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 Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25 |
-Non-polymers , 3 types, 385 molecules
#5: Chemical | #6: Chemical | ChemComp-DAD / | #7: 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: 2.99 Å3/Da / Density % sol: 58.57 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, ammonium sulfate, aces, ethylene glycol, DTT , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 12, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 44960 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.4→2.49 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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