5K52 Metal Binding Protein date May 23, 2016
title Crystal Structures Of Aldehyde Deformylating Oxygenase From Sp. Knua012
authors A.K.Park, H-.W.Kim
compound source
Molecule: Aldehyde Decarbonylase
Chain: A, B, C, D
Synonym: Ad,Fatty Aldehyde Decarbonylase
Ec: 4.1.99.5
Engineered: Yes
 Organism_scientific: Limnothrix Sp. Knua012
Organism_taxid: 1162714
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43
R_factor 0.210 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.658 135.658 71.795 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand OCD enzyme Lyase E.C.4.1.99.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal structures of aldehyde deformylating oxygenase from Limnothrix sp. KNUA012 and Oscillatoria sp. KNUA011., Park AK, Kim IS, Jeon BW, Roh SJ, Ryu MY, Baek HR, Jo SW, Kim YS, Park H, Lee JH, Yoon HS, Kim HW, Biochem Biophys Res Commun. 2016 Aug 26;477(3):395-400. doi:, 10.1016/j.bbrc.2016.06.090. Epub 2016 Jun 18. PMID:27329814
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (5k52.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (5k52.pdb2.gz) 37 Kb
  • Biological Unit Coordinates (5k52.pdb3.gz) 38 Kb
  • Biological Unit Coordinates (5k52.pdb4.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 5K52
  • CSU: Contacts of Structural Units for 5K52
  • Structure Factors (1070 Kb)
  • Retrieve 5K52 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5K52 from S2C, [Save to disk]
  • Re-refined 5k52 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5K52 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 5K52
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5k52] [5k52_A] [5k52_C] [5k52_B] [5k52_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5K52
  • Community annotation for 5K52 at PDBWiki (http://pdbwiki.org)

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