1OGP | pdb_00001ogp

The crystal structure of plant sulfite oxidase provides insight into sulfite oxidation in plants and animals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1OGP

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of Plant Sulfite Oxidase Provides Insights Into Sulfite Oxidation in Plants and Animals

Schrader, N.Fischer, K.Theis, K.Mendel, R.R.Schwarz, G.Kisker, C.

(2003) Structure 11: 1251

  • DOI: https://doi.org/10.1016/j.str.2003.09.001
  • Primary Citation Related Structures: 
    1OGP

  • PubMed Abstract: 

    The molybdenum cofactor (Moco) containing sulfite oxidase (SO) from Arabidopsis thaliana has recently been identified and biochemically characterized. The enzyme is found in peroxisomes and believed to detoxify excess sulfite that is produced during sulfur assimilation, or due to air pollution. Plant SO (PSO) is homodimeric and homologous to animal SO, but contains only a single Moco domain without an additional redox center. Here, we present the first crystal structure of a plant Moco enzyme, the apo-state of Arabidopsis SO at 2.6 A resolution. The overall fold and coordination of the Moco are similar to chicken SO (CSO). Comparisons of conserved surface residues and the charge distribution in PSO and CSO reveal major differences near the entrance to both active sites reflecting different electron acceptors. Arg374 has been identified as an important substrate binding residue due to its conformational change when compared to the sulfate bound structure of CSO.


  • Organizational Affiliation
    • Department of Pharmacological Sciences, Center for Structural Biology, State University of New York at Stony Brook, Stony Brook, NY 11794, USA.

Macromolecule Content 

  • Total Structure Weight: 265.54 kDa 
  • Atom Count: 18,888 
  • Modeled Residue Count: 2,328 
  • Deposited Residue Count: 2,358 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SULFITE OXIDASE
A, B, C, D, E
A, B, C, D, E, F
393Arabidopsis thalianaMutation(s): 0 
EC: 1.8.3.1
UniProt
Find proteins for Q9S850 (Arabidopsis thaliana)
Explore Q9S850 
Go to UniProtKB:  Q9S850
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S850
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MTQ

Query on MTQ



Download:Ideal Coordinates CCD File
DA [auth F]
J [auth A]
N [auth B]
R [auth C]
V [auth D]
DA [auth F],
J [auth A],
N [auth B],
R [auth C],
V [auth D],
Z [auth E]
(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(VI)
C10 H8 Mo N5 O8 P S2
IXNYCVJPVGNGQC-NRYJBHHQSA-L
CS

Query on CS



Download:Ideal Coordinates CCD File
AA [auth F]
BA [auth F]
G [auth A]
H [auth A]
K [auth B]
AA [auth F],
BA [auth F],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
S [auth D],
T [auth D],
W [auth E],
X [auth E]
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
CA [auth F]
I [auth A]
M [auth B]
Q [auth C]
U [auth D]
CA [auth F],
I [auth A],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.918α = 90
b = 351.271β = 90
c = 158.282γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
BEASTphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description