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 Diffractionresolution 1.89 Å
ligand 8OG, ZN enzyme Hydrolase E.C.3.2.2.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceEncounter 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] (64 Kb) [Save to disk]
  • Biological Unit Coordinates (3go8.pdb1.gz) 57 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
  • 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 3GO8, from MSDmotif at EBI
  • Fold representative 3go8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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