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Yorodumi- PDB-1sks: Binary 3' complex of T7 DNA polymerase with a DNA primer/template... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sks | ||||||
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Title | Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template | ||||||
Components |
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Keywords | TRANSFERASE/ELECTRON TRANSPORT/DNA / DNA polymerase / lesion bypass / fidelity / 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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Remark 600 | HETEROGEN THERE IS A DD-ATP PRESENT IN THE CRYSTAL BUT NO DENSITY FOR IT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sks.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sks.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 1sks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sks_validation.pdf.gz | 463.9 KB | Display | wwPDB validaton report |
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Full document | 1sks_full_validation.pdf.gz | 485.4 KB | Display | |
Data in XML | 1sks_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 1sks_validation.cif.gz | 47.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/1sks ftp://data.pdbj.org/pub/pdb/validation_reports/sk/1sks | 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: 6426.177 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 7922.077 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 / 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 , 2 types, 198 molecules
#5: Chemical | ChemComp-MG / |
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#6: 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: 3.1 Å3/Da / Density % sol: 60.07 % |
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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: CHESS / Beamline: F1 / Wavelength: 0.916 |
Detector | Detector: CCD / Date: Jul 19, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 53547 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 24.1 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.052 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.239 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 27.4214 Å2 / ksol: 0.303075 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 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: 0.015 / Total num. of bins used: 6
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