3GQ4	Lyase Dna	date	Mar 23, 2009
title	Sequence-Matched Mutm Lesion Recognition Complex 5 (Lrc5)
authors	M.C.Spong, Y.Qi, G.L.Verdine
compound		source
Molecule: Dna Glycosylase Chain: A Ec: 4.2.99.18 Engineered: Yes Mutation: Yes		Organism_scientific: Geobacillus Stearothermophilus Organism_common: Geobacillus Stearothermophilus Organism_taxid: 1422 Gene: Mutm Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet24b
Molecule: Dna (5'-D(Apgpgptpapgpapcpcpcpgpgpap 3'); Chain: B Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Tpgpcpgptpcpcpgp(8og) Pgptpcptpapcpc)-3'); Chain: C Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 21 21 21	R_factor 0.171 R_Free 0.192
crystal cell	length a length b length c angle alpha angle beta angle gamma 44.858 95.276 101.732 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	8OG, GOL, ZN	enzyme	Lyase E.C.4.2.99.18 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] (66 Kb) [Save to disk] Biological Unit Coordinates (3gq4.pdb1.gz) 60 Kb LPC: Ligand-Protein Contacts for 3GQ4 CSU: Contacts of Structural Units for 3GQ4 Structure Factors (324 Kb) Retrieve 3GQ4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GQ4 from S2C, [Save to disk] Re-refined 3gq4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GQ4 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 3GQ4

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 3GQ4, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3gq4] [3gq4_A] [3gq4_B] [3gq4_C] SWISS-PROT database: [P84131] Domain organization of [P84131_BACST] by SWISSPFAM Domains found in 3GQ4: [Fapy_DNA_glyco] [H2TH ] by SMART

Other resources with information on 3GQ4

Community annotation for 3GQ4 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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