3GPP Lyase Dna date Mar 23, 2009
title Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog) Lesion T224p Complex
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(Pgpgptpapgpaptpcpcpgpgpapc
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Pcpgptpcpcp(8og)Pgpaptpcptp
Chain: C
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.196 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.243 93.841 103.405 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand 8OG, ZN enzyme Lyase E.C.4.2.99.18 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] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (3gpp.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 3GPP
  • CSU: Contacts of Structural Units for 3GPP
  • Structure Factors (198 Kb)
  • Retrieve 3GPP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GPP from S2C, [Save to disk]
  • Re-refined 3gpp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GPP 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 3GPP
  • 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 3GPP, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gpp_A] [3gpp] [3gpp_C] [3gpp_B]
  • SWISS-PROT database: [P84131]
  • Domain organization of [P84131_BACST] by SWISSPFAM
  • Domains found in 3GPP: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 3GPP
  • Community annotation for 3GPP 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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