1MJ4

Crystal Structure Analysis of the cytochrome b5 domain of human sulfite oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The 1.2 A structure of the human sulfite oxidase cytochrome b(5) domain.

Rudolph, M.J.Johnson, J.L.Rajagopalan, K.V.Kisker, C.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1183-1191

  • DOI: 10.1107/s0907444903009934
  • Primary Citation of Related Structures:  
    1MJ4

  • PubMed Abstract: 
  • The molybdenum- and iron-containing enzyme sulfite oxidase catalyzes the physiologically vital oxidation of sulfite to sulfate. Sulfite oxidase contains three domains: an N-terminal cytochrome b(5) domain, a central domain harboring the molybdenum cofactor (Moco) and a C-terminal dimerization domain ...

    The molybdenum- and iron-containing enzyme sulfite oxidase catalyzes the physiologically vital oxidation of sulfite to sulfate. Sulfite oxidase contains three domains: an N-terminal cytochrome b(5) domain, a central domain harboring the molybdenum cofactor (Moco) and a C-terminal dimerization domain. Oxidation of the substrate sulfite is coupled to the transfer of two electrons to the molybdenum cofactor. Subsequently, these electrons are passed on, one at a time, to the b(5) heme of sulfite oxidase and from there to the soluble electron carrier cytochrome c. The crystal structure of the oxidized human sulfite oxidase cytochrome b(5) domain has been determined at 1.2 A resolution and has been refined to a crystallographic R factor of 0.107 (R(free) = 0.137). A comparison of this structure with other b(5)-type cytochromes reveals distinct structural features present in the sulfite oxidase b(5) domain which promote optimal electron transport between the Moco of sulfite oxidase and the heme of cytochrome c.


    Organizational Affiliation

    Department of Pharmacological Sciences and Center for Structural Biology, State University of New York at Stony Brook, Stony Brook, New York 11794-5115, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
sulfite oxidase A82Homo sapiensMutation(s): 0 
Gene Names: SUOX
EC: 1.8.3.1
Find proteins for P51687 (Homo sapiens)
Explore P51687 
Go to UniProtKB:  P51687
NIH Common Fund Data Resources
PHAROS:  P51687
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.899α = 90
b = 35.447β = 93.78
c = 26.263γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-12
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance