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Yorodumi- PDB-1sl2: Ternary 5' complex of T7 DNA polymerase with a DNA primer/templat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sl2 | ||||||
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Title | Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide | ||||||
Components |
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Keywords | TRANSFERASE/ELECTRON TRANSPORT/DNA / DNA polymerase / fidelity / lesion bypass / thymine dimer / 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 / 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: 2.3 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 | 1sl2.cif.gz | 185.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sl2.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 1sl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sl2_validation.pdf.gz | 837.7 KB | Display | wwPDB validaton report |
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Full document | 1sl2_full_validation.pdf.gz | 853.8 KB | Display | |
Data in XML | 1sl2_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 1sl2_validation.cif.gz | 46.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/1sl2 ftp://data.pdbj.org/pub/pdb/validation_reports/sl/1sl2 | HTTPS FTP |
-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: 6739.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer |
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#2: DNA chain | Mass: 7922.077 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, 227 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: 3.16 Å3/Da / Density % sol: 60.73 % |
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Crystal grow | pH: 7.5 / Details: VAPOR DIFFUSION, HANGING DROP, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 |
Detector | Detector: CCD / Date: Jul 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 52685 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 27.6 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 0.089 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 5.88 / Rsym value: 0.338 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.8884 Å2 / ksol: 0.338115 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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