4G4O Hydrolase Dna date Jul 16, 2012
title Mutm Containing M77a Mutation Bound To Oxog-Containing Dna
authors R.J.Sung, M.Zhang, Y.Qi, G.L.Verdine
compound source
Molecule: Formamidopyrimidine-Dna Glycosylase
Chain: A
Fragment: Mutm
Synonym: Fapy-Dna Glycosylase, Dna-(Apurinic Or Apyrimidini Lyase Mutm;
Ec: 3.2.2.23
Engineered: Yes
Mutation: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Gene: Mutm
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Papgpgptpapgpapcptpcpgpgpapcpgpc)-3');
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Tpgpcpgptpcpcp(8og)Papgp(Tx2 Pcptpapcpc)-3');
Chain: C
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.175 R_Free 0.211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.188 93.541 104.650 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand 8OG, TX2, ZN enzyme Hydrolase E.C.3.2.2.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural and biochemical analysis of DNA helix-invasion by the bacterial 8-oxoguanine DNA glycosylase MutM., Sung RJ, Zhang M, Qi Y, Verdine GL, J Biol Chem. 2013 Feb 12. PMID:23404556
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (4g4o.pdb1.gz) 112 Kb
  • LPC: Ligand-Protein Contacts for 4G4O
  • CSU: Contacts of Structural Units for 4G4O
  • Structure Factors (307 Kb)
  • Retrieve 4G4O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4G4O from S2C, [Save to disk]
  • Re-refined 4g4o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4G4O 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 4G4O
  • 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 4G4O, from MSDmotif at EBI
  • Fold representative 4g4o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4g4o_C] [4g4o_B] [4g4o_A] [4g4o]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4G4O: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 4G4O
  • Community annotation for 4G4O at PDBWiki (http://pdbwiki.org)

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