1VJE

Crystal structure of a autoinducer-2 synthesis protein with bound selenomethionine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

A Structural Genomics Approach to the Study of Quorum Sensing: Crystal Structures of Three LuxS Orthologs

Lewis, H.A., Furlong, E.B., Laubert, B., Eroshkina, G.A., Batiyenko, Y., Adams, J.M., Bergseid, M.G., Marsh, C.D., Peat, T.S., Sanderson, W.E., Sauder, J.M., Buchanan, S.G.

(2001) Structure 9: 527-537

  • DOI: https://doi.org/10.1016/s0969-2126(01)00613-x
  • Primary Citation of Related Structures:  
    1INN, 1J6V, 1J6W, 1J6X, 1VJE

  • PubMed Abstract: 

    • Quorum sensing is the mechanism by which bacteria control gene expression in response to cell density. Two major quorum-sensing systems have been identified, system 1 and system 2, each with a characteristic signaling molecule (autoinducer-1, or AI-1, in the case of system 1, and AI-2 in system 2) ...

    Quorum sensing is the mechanism by which bacteria control gene expression in response to cell density. Two major quorum-sensing systems have been identified, system 1 and system 2, each with a characteristic signaling molecule (autoinducer-1, or AI-1, in the case of system 1, and AI-2 in system 2). The luxS gene is required for the AI-2 system of quorum sensing. LuxS and AI-2 have been described in both Gram-negative and Gram-positive bacterial species and have been shown to be involved in the expression of virulence genes in several pathogens.

    Related Citations: 
    • Structural analysis of a set of proteins resulting from a bacterial genomics project
      Badger, J., Sauder, J.M., Adams, J.M., Antonysamy, S., Bain, K., Bergseid, M.G., Buchanan, S.G., Buchanan, M.D., Batiyenko, Y., Christopher, J.A., Emtage, S., Eroshkina, A., Feil, I., Furlong, E.B., Gajiwala, K.S., Gao, X., He, D., Hendle, J., Huber, A., Hoda, K., Kearins, P., Kissinger, C., Laubert, B., Lewis, H.A., Lin, J., Loomis, K., Lorimer, D., Louie, G., Maletic, M., Marsh, C.D., Miller, I., Molinari, J., Muller-Dieckmann, H.J., Newman, J.M., Noland, B.W., Pagarigan, B., Park, F., Peat, T.S., Post, K.W., Radojicic, S., Ramos, A., Romero, R., Rutter, M.E., Sanderson, W.E., Schwinn, K.D., Tresser, J., Winhoven, J., Wright, T.A., Wu, L., Xu, J., Harris, T.J.
      (2005) Proteins 60: 787
    Organizational Affiliation: 

    Structural GenomiX, San Diego, CA 92121, USA. hal_lewis@stromix.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Autoinducer-2 production protein LuxS
A, B
166Deinococcus radioduransMutation(s): 1 
Gene Names: luxS, DR2387
EC: 3.13.1 (PDB Primary Data), 4.4.1.21 (UniProt)
UniProt
Find proteins for Q9RRU8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RRU8 
Go to UniProtKB:  Q9RRU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RRU8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MSE
Query on MSE
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		SELENOMETHIONINE
C5 H11 N O2 Se
RJFAYQIBOAGBLC-BYPYZUCNSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.548α = 90
b = 81.917β = 102.81
c = 49.327γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMACrefinement
CCP4data scaling
TRUNCATEdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-10
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description