1GOX

REFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Refined structure of spinach glycolate oxidase at 2 A resolution.

Lindqvist, Y.

(1989) J Mol Biol 209: 151-166

  • DOI: 10.1016/0022-2836(89)90178-2
  • Primary Citation of Related Structures:  
    1GOX

  • PubMed Abstract: 
  • The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18 ...

    The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was obtained for 32,888 independent reflections from 5.5 to 2 A resolution. The geometry of the model, consisting of 350 amino acid residues, the cofactor flavin mononucleotide and 298 solvent molecules, is close to ideal with root-mean-square deviations of 0.015 A in bond lengths and 2.6 degrees in bond angles. The expected trimodal distribution with preference for staggered conformation is obtained for the side-chain chi 1-angles. The core of the subunit is built up from the eight beta-strands in the beta/alpha-barrel. This core consists of two hydrophobic layers. One in the center is made up of residues pointing in from the beta-strands towards the barrel axis and the second, consisting of two segments of residues, pointing out from the beta-strands towards the eight alpha-helices of the barrel and pointing from the helices towards the strands. The hydrogen bond pattern for the beta-strands in the beta/alpha-barrel is described. There are a number of residues with 3(10)-helix conformation, in particular there is one left-handed helix. The ordered solvent molecules are organized mainly in clusters. The average isotropic temperature factor is quite high, 27.1 A2, perhaps a reflection of the high solvent content in the crystal. The octameric glycolate oxidase molecule, which has 422 symmetry, makes strong interactions around the 4-fold axis forming a tight tetramer, but only weak interactions between the two tetramers forming the octamer.


    Related Citations: 
    • The Active Site of Spinach Glycolate Oxidase
      Lindqvist, Y., Branden, C.-I.
      (1989) J Biol Chem 264: 3624
    • Primary Structure of Glycolate Oxidase from Spinach
      Cederlund, E., Lindqvist, Y., Soderlund, G., Branden, C.-I., Jornvall, H.
      (1988) Eur J Biochem 173: 523
    • Structure of Glycolate Oxidase from Spinach
      Lindqvist, Y., Branden, C.-I.
      (1985) Proc Natl Acad Sci U S A 82: 6855
    • Structure of Glycolate Oxidase from Spinach at a Resolution of 5.5 Angstroms
      Lindqvist, Y., Branden, C.-I.
      (1980) J Mol Biol 143: 201
    • Preliminary Crystallographic Data for Glycolate Oxidase from Spinach
      Lindqvist, Y., Branden, C.-I.
      (1979) J Biol Chem 254: 7403

    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
(S)-2-HYDROXY-ACID OXIDASE, PEROXISOMALA370Spinacia oleraceaMutation(s): 0 
EC: 1.1.3.1 (PDB Primary Data), 1.1.3.15 (UniProt)
UniProt
Find proteins for P05414 (Spinacia oleracea)
Explore P05414 
Go to UniProtKB:  P05414
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05414
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.189 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.1α = 90
b = 148.1β = 90
c = 135.1γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 1989-06-14 
  • Released Date: 1989-10-15 
  • Deposition Author(s): Lindqvist, Y.

Revision History  (Full details and data files)

  • Version 1.0: 1989-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance