2YG9 Hydrolase date Apr 11, 2011
title Structure Of An Unusual 3-Methyladenine Dna Glycosylase II ( Deinococcus Radiodurans
authors E.Moe, D.R.Hall, I.Leiros, V.Talstad, J.Timmins, S.Mcsweeney
compound source
Molecule: Dna-3-Methyladenine Glycosidase II, Putative
Chain: A, B
Engineered: Yes
 Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
Gene: Dr_2584
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Codonplus
symmetry Space Group: C 1 2 1
R_factor 0.170 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.311 51.372 90.039 90.00 99.71 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand CL, GOL, NI enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans., Moe E, Hall DR, Leiros I, Monsen VT, Timmins J, McSweeney S, Acta Crystallogr D Biol Crystallogr. 2012 Jun;68(Pt 6):703-12. Epub 2012 May 17. PMID:22683793
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (2yg9.pdb1.gz) 39 Kb
  • Biological Unit Coordinates (2yg9.pdb2.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 2YG9
  • CSU: Contacts of Structural Units for 2YG9
  • Structure Factors (500 Kb)
  • Retrieve 2YG9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YG9 from S2C, [Save to disk]
  • Re-refined 2yg9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2YG9 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 2YG9
  • 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 2YG9, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yg9_A] [2yg9] [2yg9_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2YG9: [ENDO3c] [HhH1 ] by SMART
    • Other resources with information on 2YG9
  • Community annotation for 2YG9 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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