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: 5'-D(Gpgpgpgpgpapapgpgpaptptpapt)-3 Chain: D Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Tpcpaptpgpapaptpcpcptptpcpcpc 3'; Chain: E Engineered: Yes		Synthetic: Yes
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
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 Diffraction	resolution	2.25 Å
ligand	BAP, CA, EDO, GOL, POP	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	A 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] (77 Kb) [Save to disk] Biological Unit Coordinates (2ibk.pdb1.gz) 72 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

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 2IBK, from MSDmotif at EBI

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)

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