1SL0 Transferase Electron Transport Dna date Mar 05, 2004
title Ternary 3' Complex Of T7 Dna Polymerase With A Dna Primerte Containing A Disordered Cis-Syn Thymine Dimer On The Templa Incoming Nucleotide
authors Y.Li, S.Dutta, S.Doublie, H.M.Bdour, J.S.Taylor, T.Ellenberger
compound source
Molecule: 5'-D(Cpgpapapapapcpgpapcpgpgpcpcpa Cpcp(2dt))-3';
Chain: P, Q
Engineered: Yes
Other_details: Dna Primer
 Synthetic: Yes

Molecule: 5'-D(Cpcpcp(Ttd) Papgpgpcpapcptpgpgpcpcpgptpcpgptptptptp
Chain: T, U
Engineered: Yes
Other_details: Dna Template
Synthetic: Yes

Molecule: Dna Polymerase
Chain: A, C
Synonym: T7 Dna Polymerase
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage T7
Organism_taxid: 10760
Gene: 5
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Thioredoxin 1
Chain: B, D
Synonym: Trx1, Trx
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Trxa, Tsnc, Fipa, B3781, C4701, Z5291, Ecs4714, Stm39 Stmd1.75, Sty3639, T3381, Sf3854, S3905;
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.282 R_Free 0.351
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.266 105.466 213.931 90.00 91.57 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand 2DT, DAD, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


    • D, B
  • DNA polymerase processivity ...


    • Primary referenceNucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7., Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T, Nat Struct Mol Biol 2004 Aug;11(8):784-90. Epub 2004 Jul 4. PMID:15235589
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (229 Kb) [Save to disk]
  • Biological Unit Coordinates (1sl0.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (1sl0.pdb2.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 1SL0
  • CSU: Contacts of Structural Units for 1SL0
  • Likely Quarternary Molecular Structure file(s) for 1SL0
  • Structure Factors (323 Kb)
  • Retrieve 1SL0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SL0 from S2C, [Save to disk]
  • Re-refined 1sl0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1SL0 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1SL0
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1SL0, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1sl0a1, region A:1-210 [Jmol] [rasmolscript] [script source]
        - Domain d1sl0a2, region A:211-704 [Jmol] [rasmolscript] [script source]
        - Domain d1sl0b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1sl0c1, region C:1-210 [Jmol] [rasmolscript] [script source]
        - Domain d1sl0c2, region C:211-704 [Jmol] [rasmolscript] [script source]
        - Domain d1sl0d_, region D [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1sl0_T] [1sl0_A] [1sl0_U] [1sl0_Q] [1sl0_P] [1sl0_C] [1sl0] [1sl0_D] [1sl0_B]
  • SWISS-PROT database: [P00581] [P0AA25]
  • Domain organization of [DPOL_BPT7] [THIO_ECOLI] by SWISSPFAM
  • Domain found in 1SL0: [POLAc ] by SMART
    • Other resources with information on 1SL0
  • Community annotation for 1SL0 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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