1XQP Lyase date Oct 13, 2004
title Crystal Structure Of 8-Oxoguanosine Complexed Pa-Agog, 8-Oxo Dna Glycosylase From Pyrobaculum Aerophilum
authors G.M.Lingaraju, A.A.Sartori, D.Kostrewa, A.E.Prota, J.Jiricny, F.K
compound source
Molecule: 8-Oxoguanine Dna Glycosylase
Chain: A
Engineered: Yes
 Organism_scientific: Pyrobaculum Aerophilum
Organism_taxid: 13773
Gene: Pa-Agog
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28c(+)
symmetry Space Group: P 21 21 2
R_factor 0.183 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.220 98.110 36.170 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.69 Å
ligand 8HG enzyme
related structures by homologous chain: 1XQO
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure., Lingaraju GM, Sartori AA, Kostrewa D, Prota AE, Jiricny J, Winkler FK, Structure. 2005 Jan;13(1):87-98. PMID:15642264
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (1xqp.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 1XQP
  • CSU: Contacts of Structural Units for 1XQP
  • Likely Quarternary Molecular Structure file(s) for 1XQP
  • Structure Factors (208 Kb)
  • Retrieve 1XQP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XQP from S2C, [Save to disk]
  • Re-refined 1xqp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1XQP 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 1XQP
  • 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 1XQP, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1xqpa_, region A [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xqp_A] [1xqp]
  • SWISS-PROT database: [Q8ZVK6]
  • Domain organization of [AGOG_PYRAE] by SWISSPFAM
    • Other resources with information on 1XQP
  • Community annotation for 1XQP 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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