6GXS

Crystal structure of CV39L lectin from Chromobacterium violaceum at 1.8 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Characterization of novel lectins from Burkholderia pseudomallei and Chromobacterium violaceum with seven-bladed beta-propeller fold.

Sykorova, P.Novotna, J.Demo, G.Pompidor, G.Dubska, E.Komarek, J.Fujdiarova, E.Houser, J.Haronikova, L.Varrot, A.Shilova, N.Imberty, A.Bovin, N.Pokorna, M.Wimmerova, M.

(2020) Int J Biol Macromol 152: 1113-1124

  • DOI: https://doi.org/10.1016/j.ijbiomac.2019.10.200
  • Primary Citation of Related Structures:  
    6GXR, 6GXS

  • PubMed Abstract: 

    Burkholderia pseudomallei and Chromobacterium violaceum are bacteria of tropical and subtropical soil and water that occasionally cause fatal infections in humans and animals. Microbial lectins mediate the adhesion of organisms to host cells, which is the first phase in the development of infection. Here we report the discovery of two novel lectins from the above-mentioned bacteria - BP39L and CV39L. The crystal structures revealed that the lectins possess a seven-bladed β-propeller fold. Functional studies conducted on a series of oligo- and polysaccharides confirmed the preference of BP39L for mannosylated saccharides and CV39L for rather more complex polysaccharides with a monosaccharide preference for β-l-fucose. The presented data indicate that the proteins belong to a currently unknown family of lectins.


  • Organizational Affiliation

    Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CV39L lectin
A, B, C, D
376Chromobacterium violaceum ATCC 12472Mutation(s): 0 
Gene Names: CV_1052
UniProt
Find proteins for Q7NZ70 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757))
Explore Q7NZ70 
Go to UniProtKB:  Q7NZ70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NZ70
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
N [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
L [auth B],
M [auth B],
S [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
T [auth D],
U [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.709α = 90
b = 123.781β = 90
c = 180.935γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic13-25401S
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicCEITEC 2020 (LQ1601)

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references