[English] 日本語
Yorodumi- PDB-1sl1: Binary 5' complex of T7 DNA polymerase with a DNA primer/template... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sl1 | ||||||
---|---|---|---|---|---|---|---|
Title | Binary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template | ||||||
Components |
| ||||||
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 |
| ||||||
Remark 600 | HETEROGEN THERE IS A DD-ATP PRESENT IN THE CRYSTAL BUT NO DENSITY FOR IT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1sl1.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1sl1.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 1sl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/1sl1 ftp://data.pdbj.org/pub/pdb/validation_reports/sl/1sl1 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#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 |
---|---|
#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 , 2 types, 240 molecules
#5: Chemical | ChemComp-MG / |
---|---|
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.51 % |
---|---|
Crystal grow | pH: 7.5 / Details: VAPOR DIFFUSION, HANGING DROP, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.2→50 Å / Num. obs: 60347 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 25.2 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.068 / Net I/σ(I): 36.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 6.69 / Rsym value: 0.309 / % possible all: 99.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.0504 Å2 / ksol: 0.341313 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
|