1YCL Hydrolase date Dec 22, 2004
title Crystal Structure Of B. Subtilis Luxs In Complex With A Cata Ketone Intermediate
authors R.Rajan, J.Zhu, X.Hu, D.Pei, C.E.Bell
compound source
Molecule: S-Ribosylhomocysteinase
Chain: A
Synonym: Autoinducer-2 Production Protein Luxs, Ai-2 Synthe Protein;
Ec: 3.13.1.-
Engineered: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Gene: Luxs
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 65 2 2
R_factor 0.225 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.530 62.530 149.650 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.80 Å
ligand CO, KRI, SO4 enzyme Hydrolase E.C.3.13.1 BRENDA
related structures by homologous chain: 1IE0, 1JVI
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal Structure of S-Ribosylhomocysteinase (LuxS) in Complex with a Catalytic 2-Ketone Intermediate(,)., Rajan R, Zhu J, Hu X, Pei D, Bell CE, Biochemistry 2005 Mar 15;44(10):3745-53. PMID:15751951
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (32 Kb) [Save to disk]
  • Biological Unit Coordinates (1ycl.pdb1.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 1YCL
  • CSU: Contacts of Structural Units for 1YCL
  • Likely Quarternary Molecular Structure file(s) for 1YCL
  • Structure Factors (164 Kb)
  • Retrieve 1YCL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YCL from S2C, [Save to disk]
  • Re-refined 1ycl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YCL 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 1YCL
  • 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 1YCL, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ycl] [1ycl_A]
  • SWISS-PROT database: [O34667]
  • Domain organization of [LUXS_BACSU] by SWISSPFAM
  • Other resources with information on 1YCL
  • Community annotation for 1YCL 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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