4Z8B

crystal structure of a DGL mutant - H51G H131N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.951 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Quaternary structure of Dioclea grandiflora lectin assessed by equilibrium sedimentation and crystallographic analysis of recombinant mutants.

Zamora-Caballero, S.Perez, A.Sanz, L.Bravo, J.Calvete, J.J.

(2015) Febs Lett. 589: 2290-2296

  • DOI: 10.1016/j.febslet.2015.07.020

  • PubMed Abstract: 
  • The structural basis of the pH dependency of the dimer-tetramer transition exhibited by Brinda's type II Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of recombinant wild-type and site-dire ...

    The structural basis of the pH dependency of the dimer-tetramer transition exhibited by Brinda's type II Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of recombinant wild-type and site-directed single and double mutants of the pH-stable tetrameric Dioclea grandiflora lectin (r-αDGL). Releasing the peripheral site interdimeric contact between R60 and D78 rendered a mutant displaying dimer-tetramer equilibrium in the pH range equivalent to pKa±1 of the γ-COOH. Mutation of both histidines 51 and 131, but not the mutation of each His separately, abolished the formation of the Diocleinae canonical tetramer in the pH range 2.5-8.5. The X-ray structure of the double mutant r-αDGL H51G/H131N suggests that H131 plays a crucial role in networking loop 114-125 residues from all four subunits at the central cavity of the tetrameric lectin, and that H51 maintains the central cavity loops in a proper spatial orientation to make H131-mediated interdimer contacts.


    Organizational Affiliation

    Unidad de Transducción de Señales, Instituto de Biomedicina de Valencia, CSIC, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lectin alpha chain
A
237Dioclea grandifloraMutation(s): 0 
Find proteins for P08902 (Dioclea grandiflora)
Go to UniProtKB:  P08902
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
XMM
Query on XMM

Download SDF File 
Download CCD File 
A
(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL
(5-BROMO-4-CHLORO-3-INDOLYL)-A-D-MANNOSE
C14 H15 Br Cl N O6
OPIFSICVWOWJMJ-HAAGFXOZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.951 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 62.350α = 90.00
b = 67.080β = 90.00
c = 108.620γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
iMOSFLMdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2015-08-19
    Type: Database references