5EO7 | pdb_00005eo7

Crystal structure of AOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.241 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Six independent fucose-binding sites in the crystal structure of Aspergillus oryzae lectin

Makyio, H.Shimabukuro, J.Suzuki, T.Imamura, A.Ishida, H.Kiso, M.Ando, H.Kato, R.

(2016) Biochem Biophys Res Commun 477: 477-482

  • DOI: https://doi.org/10.1016/j.bbrc.2016.06.069
  • Primary Citation Related Structures: 
    5EO7, 5EO8

  • PubMed Abstract: 

    The crystal structure of AOL (a fucose-specific lectin of Aspergillus oryzae) has been solved by SAD (single-wavelength anomalous diffraction) and MAD (multi-wavelength anomalous diffraction) phasing of seleno-fucosides. The overall structure is a six-bladed β-propeller similar to that of other fucose-specific lectins. The fucose moieties of the seleno-fucosides are located in six fucose-binding sites. Although the Arg and Glu/Gln residues bound to the fucose moiety are common to all fucose-binding sites, the amino-acid residues involved in fucose binding at each site are not identical. The varying peak heights of the seleniums in the electron density map suggest that each fucose-binding site has a different carbohydrate binding affinity.


  • Organizational Affiliation
    • Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.

Macromolecule Content 

  • Total Structure Weight: 107.33 kDa 
  • Atom Count: 7,846 
  • Modeled Residue Count: 930 
  • Deposited Residue Count: 930 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Predicted protein
A, B, C
310Aspergillus oryzae RIB40Mutation(s): 0 
Gene Names: AO090001000189
UniProt
Find proteins for Q2UNX8 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore Q2UNX8 
Go to UniProtKB:  Q2UNX8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2UNX8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SFU

Query on SFU



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C]
methyl 1-seleno-alpha-L-fucopyranoside
C7 H14 O4 Se
VHTNTJQSKJZERS-XUVCUMPTSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A],
V [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.241 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.161α = 90
b = 196.852β = 90
c = 110.605γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
SHARPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2024-03-20
    Changes: Data collection, Database references, Structure summary