2XZF Hydrolase Dna date Nov 25, 2010
title Crystal Structure Of A Complex Between The Wild-Type Lactococcus Lactis Fpg (Mutm) And An Oxidized Pyrimidine Containing Dna At 293k
authors Y.V.Lebihan, M.A.Izquierdo, F.Coste, F.Culard, T.H.Gehrke, K.Essa P.Aller, T.Carrel, B.Castaing
compound source
Molecule: Formamidopyrimidine-Dna Glycosylase
Chain: A
Synonym: Fapy-Dna Glycosylase
Ec: 3.2.2.23
Engineered: Yes
Organism_scientific: Lactococcus Lactis Subsp. Cremoris
Organism_taxid: 1359
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmal-C

Molecule: 5'-D(Cptpcptptptpvetptptptpcptpcpgp
Chain: B

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Gpapgpapapapcpapapapgpapgpcp)-
Chain: C

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.1595 R_Free 0.1911
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.569 91.569 142.777 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand GOL, VET, ZN enzyme Hydrolase E.C.3.2.2.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary reference5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases., Le Bihan YV, Angeles Izquierdo M, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carell T, Castaing B, Nucleic Acids Res. 2011 Aug;39(14):6277-90. Epub 2011 Apr 12. PMID:21486746
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (130 Kb) [Save to disk]
  • Biological Unit Coordinates (2xzf.pdb1.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 2XZF
  • CSU: Contacts of Structural Units for 2XZF
  • Structure Factors (402 Kb)
  • Retrieve 2XZF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XZF from S2C, [Save to disk]
  • Re-refined 2xzf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XZF 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 2XZF
  • 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 2XZF, from MSDmotif at EBI
  • Fold representative 2xzf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xzf_A] [2xzf] [2xzf_B] [2xzf_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XZF: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 2XZF
  • Community annotation for 2XZF at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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