4J1O Isomerase date Feb 01, 2013
title Crystal Structure Of An Enolase (Mandelate Racemase Subgroup Paracococus Denitrificans Pd1222 (Target Nysgrc-012907) Wit Proline Betaine (Substrate)
authors M.W.Vetting, R.Toro, R.Bhosle, S.R.Wasserman, L.L.Morisco, S.Soji S.Chamala, A.Kar, J.Lafleur, G.Villigas, B.Evans, J.Hammonds, A.G M.Stead, B.Hillerich, J.Love, R.D.Seidel, J.B.Bonanno, J.A.Gerlt S.C.Almo, New York Structural Genomics Research Consortium (
compound source
Molecule: Mandelate Racemasemuconate Lactonizing Enzyme, N Domain Protein;
Chain: A, B
Engineered: Yes
Organism_scientific: Paracoccus Denitrificans
Organism_taxid: 318586
Strain: Pd1222
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: P 4 21 2
R_factor 0.158 R_Free 0.181
length a length b length c angle alpha angle beta angle gamma
117.297 117.297 110.528 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand GOL, IOD, MG, PBE enzyme
A, B

Primary referencePrediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine., Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE, MBio. 2014 Feb 11;5(1):e00933-13. doi: 10.1128/mBio.00933-13. PMID:24520058
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (250 Kb) [Save to disk]
  • Biological Unit Coordinates (4j1o.pdb1.gz) 963 Kb
  • LPC: Ligand-Protein Contacts for 4J1O
  • CSU: Contacts of Structural Units for 4J1O
  • Structure Factors (5384 Kb)
  • Retrieve 4J1O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4J1O from S2C, [Save to disk]
  • Re-refined 4j1o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4J1O 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 4J1O
  • 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 4J1O, from MSDmotif at EBI
  • Fold representative 4j1o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4j1o_A] [4j1o] [4j1o_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4J1O: [MR_MLE ] by SMART
  • Other resources with information on 4J1O
  • Community annotation for 4J1O at PDBWiki (http://pdbwiki.org)

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