4B9V	Transferase Dna	date	Sep 06, 2012
title	Structure Of The High Fidelity Dna Polymerase I With Extendi Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair.
authors	T.H.Gehrke, U.Lischke, S.Arnold, S.Schneider, T.Carell
compound		source
Molecule: Dna Polymerase Chain: A Synonym: Dna Polymerase I Ec: 2.7.7.7 Engineered: Yes		Organism_scientific: Geobacillus Stearothermophilus Organism_taxid: 1422 Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_vector: Pdest007 Other_details: German Collection Of Microorganisms Dsm No.
Molecule: 5'-D(Cpcptpgpapcptpcptpapap)-3' Chain: B Engineered: Yes Other_details: Oxidative Dna Lesion Fapyg At C4		Synthetic: Yes Organism_scientific: Geobacillus Stearothermophilus Organism_taxid: 1422
Molecule: 5'-D(Cpaptpfoxpapgpapgptpcpapgpgpcp Chain: C Engineered: Yes Other_details: Oxidative Dna Lesion Fapyg At C4		Synthetic: Yes Organism_scientific: Geobacillus Stearothermophilus Organism_taxid: 1422
symmetry	Space Group: P 21 21 21	R_factor 0.187 R_Free 0.215
crystal cell	length a length b length c angle alpha angle beta angle gamma 87.901 94.035 105.341 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	FOX, MG, SO4	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A DNA-directed DNA polymerase ... 3'-5' exonuclease activity
Primary reference	Unexpected non-Hoogsteen-based mutagenicity mechanism of FaPy-DNA lesions., Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T, Nat Chem Biol. 2013 May 19. doi: 10.1038/nchembio.1254. PMID:23685671

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (215 Kb) [Save to disk] Biological Unit Coordinates (4b9v.pdb1.gz) 207 Kb LPC: Ligand-Protein Contacts for 4B9V CSU: Contacts of Structural Units for 4B9V Structure Factors (358 Kb) Retrieve 4B9V in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 4B9V from S2C, [Save to disk] Re-refined 4b9v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 4B9V 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 4B9V

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 4B9V, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [4b9v_B] [4b9v_C] [4b9v_A] [4b9v] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 4B9V: [35EXOc] [POLAc ] by SMART

Other resources with information on 4B9V

Community annotation for 4B9V at PDBWiki (http://pdbwiki.org)

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