3GO8	Lyase Dna	date	Mar 18, 2009
title	Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog) Lesion Loop Deletion Complex
authors	M.C.Spong, Y.Qi, G.L.Verdine
compound		source
Molecule: Formamidopyrimidine-Dna Glycosylase Chain: A Fragment: Mutm Synonym: Fapy-Dna Glycosylase,Dna-(Apurinic Or Apyrimidinic Lyase Mutm,Ap Lyase Mutm; Ec: 3.2.2.23,4.2.99.18 Engineered: Yes Mutation: Yes		Organism_scientific: Geobacillus Stearothermophilus Organism_common: Bacillus Stearothermophilus Organism_taxid: 1422 Gene: Mutm, Fpg Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet24b
Molecule: 5'-D(Pgpgptpapgpaptpcpcpgpgpapcpg)- Chain: B Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630 Other_details: Synthetic Dna
Molecule: 5'-D(Gpcpgptpcpcp(8og)Pgpaptpcptpap Chain: C Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630 Other_details: Synthetic Dna
symmetry	Space Group: P 21 21 21	R_factor 0.185 R_Free 0.218
crystal cell	length a length b length c angle alpha angle beta angle gamma 45.244 92.655 105.246 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.89 Å
ligand	8OG, ZN	enzyme	Hydrolase E.C.3.2.2.23 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme., Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL, Nature. 2009 Dec 10;462(7274):762-6. PMID:20010681

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (63 Kb) [Save to disk] Biological Unit Coordinates (3go8.pdb1.gz) 56 Kb LPC: Ligand-Protein Contacts for 3GO8 CSU: Contacts of Structural Units for 3GO8 Structure Factors (258 Kb) Retrieve 3GO8 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GO8 from S2C, [Save to disk] Re-refined 3go8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GO8 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 3GO8

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 3GO8, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3go8_A] [3go8_C] [3go8] [3go8_B] SWISS-PROT database: [P84131] Domain organization of [P84131_BACST] by SWISSPFAM Domains found in 3GO8: [Fapy_DNA_glyco] [H2TH ] by SMART

Other resources with information on 3GO8

Community annotation for 3GO8 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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