5DIK Oxidoreductase date Sep 01, 2015
title Crystal Structure Of Apo-Lpg0406, A Carboxymuconolactone Dec Family Protein From Legionella Pneumophila
authors X.Chen, X.Gong, N.Zhang, H.Ge
compound source
Molecule: Alkyl Hydroperoxide Reductase Ahpd
Chain: A, B, C
Synonym: Alkylhydroperoxidase
Ec: 1.11.1.15
Engineered: Yes
Organism_scientific: Legionella Pneumophila
Organism_taxid: 446
Gene: Lptwr_00386, Lpymg_00422
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
symmetry Space Group: C 2 2 21
R_factor 0.183 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.797 104.806 106.750 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand
enzyme Oxidoreductase E.C.1.11.1.15 BRENDA
Gene LPTWR ; LPYMG
Gene
Ontology
ChainFunctionProcessComponent
A, C, B
  • peroxiredoxin activity


  • Primary referenceStructure of lpg0406, a carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response from Legionella pneumophila., Chen X, Hu Y, Yang B, Gong X, Zhang N, Niu L, Wu Y, Ge H, Protein Sci. 2015 Sep 24. doi: 10.1002/pro.2811. PMID:26402328
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (5dik.pdb1.gz) 106 Kb
  • CSU: Contacts of Structural Units for 5DIK
  • Structure Factors (450 Kb)
  • Retrieve 5DIK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DIK from S2C, [Save to disk]
  • Re-refined 5dik structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DIK 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 5DIK
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dik] [5dik_C] [5dik_B] [5dik_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5DIK
  • Community annotation for 5DIK at PDBWiki (http://pdbwiki.org)

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