4U2L | pdb_00004u2l

Dithionite reduced cholesterol in complex with sulfite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 
    0.133 (Depositor), 0.143 (DCC) 
  • R-Value Work: 
    0.097 (Depositor), 0.108 (DCC) 
  • R-Value Observed: 
    0.101 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4U2L

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

High-resolution structures of cholesterol oxidase in the reduced state provide insights into redox stabilization.

Golden, E.Karton, A.Vrielink, A.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3155-3166

  • DOI: https://doi.org/10.1107/S139900471402286X
  • Primary Citation Related Structures: 
    4U2L, 4U2S, 4U2T

  • PubMed Abstract: 

    Cholesterol oxidase (CO) is a flavoenzyme that catalyzes the oxidation and isomerization of cholesterol to cholest-4-en-3-one. The reductive half reaction occurs via a hydride transfer from the substrate to the FAD cofactor. The structures of CO reduced with dithionite under aerobic conditions and in the presence of the substrate 2-propanol under both aerobic and anaerobic conditions are presented. The 1.32 Å resolution structure of the dithionite-reduced enzyme reveals a sulfite molecule covalently bound to the FAD cofactor. The isoalloxazine ring system displays a bent structure relative to that of the oxidized enzyme, and alternate conformations of a triad of aromatic residues near to the cofactor are evident. A 1.12 Å resolution anaerobically trapped reduced enzyme structure in the presence of 2-propanol does not show a similar bending of the flavin ring system, but does show alternate conformations of the aromatic triad. Additionally, a significant difference electron-density peak is observed within a covalent-bond distance of N5 of the flavin moiety, suggesting that a hydride-transfer event has occurred as a result of substrate oxidation trapping the flavin in the electron-rich reduced state. The hydride transfer generates a tetrahedral geometry about the flavin N5 atom. High-level density-functional theory calculations were performed to correlate the crystallographic findings with the energetics of this unusual arrangement of the flavin moiety. These calculations suggest that strong hydrogen-bond interactions between Gly120 and the flavin N5 centre may play an important role in these structural features.


  • Organizational Affiliation
    • School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia.

Macromolecule Content 

  • Total Structure Weight: 56.95 kDa 
  • Atom Count: 5,041 
  • Modeled Residue Count: 499 
  • Deposited Residue Count: 510 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cholesterol oxidase510Streptomyces sp. SA-COOMutation(s): 0 
Gene Names: choA
EC: 1.1.3.6 (PDB Primary Data), 5.3.3.1 (PDB Primary Data)
UniProt
Find proteins for P12676 (Streptomyces sp. (strain SA-COO))
Explore P12676 
Go to UniProtKB:  P12676
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12676
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on SFD



Download:Ideal Coordinates CCD File
E [auth A](S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHOXY)(HYDROXY)PHOSPHORYLOXY)(HYDROXY)PHOSPHORYLOXY)-2,3,4-TRIHYDROXYPENTYL)-7,8-DIMETHYL-2,4-DIOXO-2,3,4,4A-TETRAHYDROBENZO[G]PTERIDINE-5(10H)-SULFONIC ACID
C27 H35 N9 O18 P2 S
WCBOBURWKHIISA-LDVRFEIFSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free:  0.133 (Depositor), 0.143 (DCC) 
  • R-Value Work:  0.097 (Depositor), 0.108 (DCC) 
  • R-Value Observed: 0.101 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.375α = 90
b = 73.565β = 105.03
c = 63.431γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2016-06-01
    Changes: Data collection
  • Version 1.4: 2017-11-22
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description