1VGX Hydrolase date Nov 03, 2003
title Crystal Structure Of A Autoinducer-2 Synthesis Protein
authors Structural Genomix
compound source
Molecule: S-Ribosylhomocysteinase
Chain: A, B
Synonym: Autoinducer-2 Production Protein Luxs, Ai-2 Synthe Protein;
Ec: 3.13.1.-
Engineered: Yes
 Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
Gene: Luxs, Dr2387
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.171 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.220 42.860 49.354 103.19 90.55 114.32
method X-Ray Diffractionresolution 1.90 Å
ligand CSD, ZN enzyme Hydrolase E.C.3.13.1 BRENDA
related structures by homologous chain: 1INN, 1VH2
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural analysis of a set of proteins resulting from a bacterial genomics project., Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ, Proteins. 2005 Sep 1;60(4):787-96. PMID:16021622
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (1vgx.pdb1.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 1VGX
  • CSU: Contacts of Structural Units for 1VGX
  • Likely Quarternary Molecular Structure file(s) for 1VGX
  • Structure Factors (257 Kb)
  • Retrieve 1VGX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VGX from S2C, [Save to disk]
  • Re-refined 1vgx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VGX 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 1VGX
  • 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 1VGX, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vgxa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vgxb_, region B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vgx_B] [1vgx_A] [1vgx]
  • SWISS-PROT database: [Q9RRU8]
  • Domain organization of [LUXS_DEIRA] by SWISSPFAM
    • Other resources with information on 1VGX
  • Community annotation for 1VGX 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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