2XY6 Transferase Dna date Nov 15, 2010
title Crystal Structure Of A Salicylic Aldehyde Basepair In Comple Fragment Dna Polymerase I From Bacillus Stearothermophilus
authors C.Kaul, M.Mueller, M.Wagner, S.Schneider, T.Carell
compound source
Molecule: Dna Polymerase I
Chain: A
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Strain: Dsm 22
Atcc: 12980
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Other_details: German Collection Of Microorganisms (Dsm)

Molecule: 5'-D(Gpapcpcpsayptpcpcpcptp)-3'
Chain: B
Synonym: Polydesoxyribonucleotide
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Apgpgpgpapsaypgpgptpcp)-3'
Chain: C
Synonym: Polydesoxyribonucleotide
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.213 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.235 93.127 105.505 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand MES, MRD, SAY, SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • 3'-5' exonuclease activity


  • Primary referenceReversible bond formation enables the replication and amplification of a crosslinking salen complex as an orthogonal base pair., Kaul C, Muller M, Wagner M, Schneider S, Carell T, Nat Chem. 2011 Aug 28;3(10):794-800. doi: 10.1038/nchem.1117. PMID:21941252
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk]
  • Biological Unit Coordinates (2xy6.pdb1.gz) 102 Kb
  • LPC: Ligand-Protein Contacts for 2XY6
  • CSU: Contacts of Structural Units for 2XY6
  • Structure Factors (304 Kb)
  • Retrieve 2XY6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XY6 from S2C, [Save to disk]
  • Re-refined 2xy6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XY6 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 2XY6
  • 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 2XY6, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xy6_C] [2xy6_A] [2xy6_B] [2xy6]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XY6: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 2XY6
  • Community annotation for 2XY6 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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