2J6U Transferase Dna date Oct 04, 2006
title Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna Polymerase, O6-Methylguanine Modified Dna, And Dgtp.
authors R.L.Eoff, A.Irimia, F.P.Guengerich, M.Egli
compound source
Molecule: Dna Polymerase Iv
Chain: A
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22bdpo4-Nhis
Other_details: Gene Dpo4

Molecule: 5'-D(Gpgpgpgpgpapapgpgpap Tptpcpt)-3';
Chain: P
Synonym: 14-Mer Primer

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Tpcpapc G32pgpapaptpcpcp Tptpcpcpcpcpc)-3';
Chain: T
Synonym: 18-Mer Template
Other_details: 5'Tcac G32 Gaatccttccccc3'

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 2
R_factor 0.217 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.318 102.285 52.485 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand 6OG, CA, DGT enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred., Eoff RL, Irimia A, Egli M, Guengerich FP, J Biol Chem. 2007 Jan 12;282(2):1456-67. Epub 2006 Nov 14. PMID:17105728
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (2j6u.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 2J6U
  • CSU: Contacts of Structural Units for 2J6U
  • Likely Quarternary Molecular Structure file(s) for 2J6U
  • Structure Factors (87 Kb)
  • Retrieve 2J6U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2J6U from S2C, [Save to disk]
  • Re-refined 2j6u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2J6U 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 2J6U
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2J6U, from MSDmotif at EBI
  • Fold representative 2j6u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2j6u] [2j6u_A] [2j6u_T] [2j6u_P]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2J6U
  • Community annotation for 2J6U 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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