3IK4 Isomerase date Aug 05, 2009
title Crystal Structure Of Mandelate Racemasemuconate Lactonizing From Herpetosiphon Aurantiacus
authors Y.Patskovsky, R.Toro, M.Dickey, M.Iizuka, J.M.Sauder, J.A.Gerlt, S.K.Burley, S.C.Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
compound source
Molecule: Mandelate Racemasemuconate Lactonizing Protein
Chain: A, B, C, D
Engineered: Yes
 Organism_scientific: Herpetosiphon Aurantiacus Atcc 23779
Organism_taxid: 316274
Gene: Haur_1114
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.217 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.026 93.344 85.914 90.00 112.60 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand GOL, K enzyme
Gene HAUR
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceHomology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily., Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP, Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. Epub 2012 Mar 5. PMID:22392983
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (215 Kb) [Save to disk]
  • Biological Unit Coordinates (3ik4.pdb1.gz) 56 Kb
  • Biological Unit Coordinates (3ik4.pdb2.gz) 57 Kb
  • Biological Unit Coordinates (3ik4.pdb3.gz) 55 Kb
  • Biological Unit Coordinates (3ik4.pdb4.gz) 54 Kb
  • Biological Unit Coordinates (3ik4.pdb5.gz) 109 Kb
  • Biological Unit Coordinates (3ik4.pdb6.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 3IK4
  • CSU: Contacts of Structural Units for 3IK4
  • Structure Factors (698 Kb)
  • Retrieve 3IK4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IK4 from S2C, [Save to disk]
  • Re-refined 3ik4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3IK4 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 3IK4
  • 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 3IK4, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ik4_D] [3ik4] [3ik4_A] [3ik4_B] [3ik4_C]
  • SWISS-PROT database: [A9B055]
  • Domain organization of [A9B055_HERA2] by SWISSPFAM
  • Domain found in 3IK4: [MR_MLE ] by SMART
    • Other resources with information on 3IK4
  • Community annotation for 3IK4 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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