2PES

Urate Oxidase in complex with tris-dipicolinate Lutetium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction.

Pompidor, G.Maury, O.Vicat, J.Kahn, R.

(2010) Acta Crystallogr D Biol Crystallogr 66: 762-769

  • DOI: 10.1107/S0907444910010954
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Tris-dipicolinate lanthanide complexes were used to prepare derivative crystals of six proteins: hen egg-white lysozyme, turkey egg-white lysozyme, thaumatin from Thaumatococcus daniellii, urate oxidase from Aspergillus flavus, porcine pancreatic ela ...

    Tris-dipicolinate lanthanide complexes were used to prepare derivative crystals of six proteins: hen egg-white lysozyme, turkey egg-white lysozyme, thaumatin from Thaumatococcus daniellii, urate oxidase from Aspergillus flavus, porcine pancreatic elastase and xylanase from Trichoderma reesei. Diffraction data were collected using either synchrotron radiation or X-rays from a laboratory source. In all cases, the complex turned out to be bound to the protein and the phases determined using the anomalous scattering of the lanthanide led to high-quality electron-density maps. The binding mode of the complex was characterized from the refined structures. The lanthanide tris-dipicolinate was found to bind through interactions between carboxylate groups of the dipicolinate ligands and hydrogen-bond donor groups of the protein. In each binding site, one enantiomeric form of the complex is selected from the racemic solution according to the specific site topology. For hen egg-white lysozyme and xylanase, derivative crystals obtained by cocrystallization belonged to a new monoclinic C2 crystal form that diffracted to high resolution.


    Organizational Affiliation

    Institut de Biologie Structurale J.-P. Ebel, UMR 5075, 41 Rue Jules Horowitz, Grenoble, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uricase
A
295Aspergillus flavusMutation(s): 0 
Gene Names: uaZuox
EC: 1.7.3.3
Find proteins for Q00511 (Aspergillus flavus)
Go to UniProtKB:  Q00511
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LU
Query on LU

Download CCD File 
A
LUTETIUM (III) ION
Lu
PSDMOPINLDTFSZ-UHFFFAOYSA-N
 Ligand Interaction
PDC
Query on PDC

Download CCD File 
A
PYRIDINE-2,6-DICARBOXYLIC ACID
C7 H5 N O4
WJJMNDUMQPNECX-UHFFFAOYSA-N
 Ligand Interaction
AZA
Query on AZA

Download CCD File 
A
8-AZAXANTHINE
C4 H3 N5 O2
KVGVQTOQSNJTJI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.55α = 90
b = 95.32β = 90
c = 104.33γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references