1PJI Hydrolase Dna date Jun 03, 2003
title Crystal Structure Of Wild Type Lactococcus Lactis Fpg Comple 1,3 Propanediol Containing Dna
authors K.Pereira, L.Serre, C.Zelwer, B.Castaing
compound source
Molecule: Dna (5'-D(Cptpcptptptp(Pdi)Ptptptpcpt 3');
Chain: D
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic

Molecule: Dna (5'-D(Gpcpgpapgpapapapcpapapapgp
Chain: E
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic

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
Strain: Subsp. Cremoris
Gene: Mutm Or Fpg
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmal-C
symmetry Space Group: P 41 21 2
R_factor 0.210 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.955 91.955 142.076 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand GOL, PDI, ZN enzyme Hydrolase E.C.3.2.2.23 BRENDA
related structures by homologous chain: 1NNJ, 1PJJ
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA., Pereira de Jesus K, Serre L, Zelwer C, Castaing B, Nucleic Acids Res. 2005 Oct 20;33(18):5936-44. Print 2005. PMID:16243784
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (1pji.pdb1.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 1PJI
  • CSU: Contacts of Structural Units for 1PJI
  • Likely Quarternary Molecular Structure file(s) for 1PJI
  • Structure Factors (362 Kb)
  • Retrieve 1PJI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PJI from S2C, [Save to disk]
  • Re-refined 1pji structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PJI 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 1PJI
  • 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 1PJI, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pjia2, region A:1-131 [Jmol] [rasmolscript] [script source]
        - Domain d1pjia1, region A:132-218 [Jmol] [rasmolscript] [script source]
        - Domain d1pjia3, region A:223-271 [Jmol] [rasmolscript] [script source]
  • Fold representative 1pji from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1pji_A] [1pji_D] [1pji_E] [1pji]
  • SWISS-PROT database: [P42371]
  • Domain organization of [FPG_LACLC] by SWISSPFAM
  • Domains found in 1PJI: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 1PJI
  • Community annotation for 1PJI 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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