3AU6 Transferase Dna date Jan 28, 2011
title Dna Polymerase X From Thermus Thermophilus Hb8 Ternary Compl Primertemplate Dna And Ddgtp
authors S.Nakane, R.Masui, S.Kuramitsu, Riken Structural Genomicsprote Initiative (Rsgi)
compound source
Molecule: Dna Polymerase Beta Family (X Family)
Chain: A
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Polx, Ttha1150
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-11a

Molecule: 5'-D(Cpapgptpaptp(Ddg))-3'
Chain: P
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Cpgpgpcpcpaptpapcptpg)-3'
Chain: T
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 43 21 2
R_factor 0.256 R_Free 0.319
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.166 80.166 268.555 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand CL, DDG, DG3, MG, SO4, ZN enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA., Nakane S, Ishikawa H, Nakagawa N, Kuramitsu S, Masui R, J Mol Biol. 2012 Mar 30;417(3):179-96. Epub 2012 Jan 27. PMID:22306405
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk]
  • Biological Unit Coordinates (3au6.pdb1.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 3AU6
  • CSU: Contacts of Structural Units for 3AU6
  • Structure Factors (134 Kb)
  • Retrieve 3AU6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AU6 from S2C, [Save to disk]
  • Re-refined 3au6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AU6 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 3AU6
  • 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 3AU6, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3au6] [3au6_T] [3au6_A] [3au6_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3AU6: [HhH1] [POLIIIAc] [POLXc ] by SMART
  • Other resources with information on 3AU6
  • Community annotation for 3AU6 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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