3JXY Hydrolase Dna date Sep 21, 2009
title Bacillus Cereus Alkylpurine Dna Glycosylase Alkd Bound To Dn Containing A Gt Mismatch
authors E.H.Rubinson, B.F.Eichman
compound source
Molecule: Alkylpurine Dna Glycosylase Alkd
Chain: A
Engineered: Yes
 Organism_scientific: Bacillus Cereus
Organism_taxid: 222523
Strain: Atcc 10987
Gene: Alkd, Bc_4913
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hms174
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbg103

Molecule: Dna (5'-D(Cpgpgpapcptpgpapcpgpgpg)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Cpcpcpgptptpapgptpcpcpg)-3'
Chain: C
Engineered: Yes
Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.130 R_Free 0.174
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.200 93.594 48.118 90.00 112.60 90.00
method X-Ray Diffractionresolution 1.50 Å
Gene BC
Primary referenceAn unprecedented nucleic acid capture mechanism for excision of DNA damage., Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman BF, Nature. 2010 Nov 18;468(7322):406-11. Epub 2010 Oct 3. PMID:20927102
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (3jxy.pdb1.gz) 118 Kb
  • CSU: Contacts of Structural Units for 3JXY
  • Structure Factors (685 Kb)
  • Retrieve 3JXY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JXY from S2C, [Save to disk]
  • Re-refined 3jxy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3JXY 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 3JXY
  • 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 3JXY, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3jxy_C] [3jxy_B] [3jxy] [3jxy_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3JXY
  • Community annotation for 3JXY 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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