2IBK Transferase Dna date Sep 11, 2006
title Bypass Of Major Benzopyrene-Dg Adduct By Y-Family Dna Polyme Unique Structural Gap
authors J.Bauer, H.Ling, J.M.Sayer, G.Xing, H.Yagi, D.M.Jerina
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
Gene: Dbh, Dpo4
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: 5'-D(Gpgpgpgpgpapapgpgpaptptpapt)-3
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Tpcpaptpgpapaptpcpcptptpcpcpc 3';
Chain: E
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.250 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
96.714 100.473 52.332 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand BAP, CA, EDO, GOL, POP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment., Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling H, Proc Natl Acad Sci U S A. 2007 Sep 18;104(38):14905-10. Epub 2007 Sep 11. PMID:17848527
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (2ibk.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 2IBK
  • CSU: Contacts of Structural Units for 2IBK
  • Likely Quarternary Molecular Structure file(s) for 2IBK
  • Structure Factors (357 Kb)
  • Retrieve 2IBK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IBK from S2C, [Save to disk]
  • Re-refined 2ibk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IBK 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 2IBK
  • 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 2IBK, from MSDmotif at EBI
  • Fold representative 2ibk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ibk_A] [2ibk] [2ibk_E] [2ibk_D]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2IBK
  • Community annotation for 2IBK 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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