1N1P

ATOMIC RESOLUTION STRUCTURE OF CHOLESTEROL OXIDASE @ pH 7.4 (STREPTOMYCES SP. SA-COO)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.119 
  • R-Value Work: 0.097 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Atomic Resolution Density Maps Reveal Secondary Structure Dependent Differences in Electronic Distribution

Lario, P.I.Vrielink, A.

(2003) J.Am.Chem.Soc. 125: 12787-12794

  • DOI: 10.1021/ja0289954

  • PubMed Abstract: 
  • The X-ray crystal structure of the flavoenzyme cholesterol oxidase, SCOA (Streptomyces sp.SA-COO) has been determined to 0.95 A resolution. The large size (55kDa) and the high-resolution diffraction of this protein provides a unique opportunity to ob ...

    The X-ray crystal structure of the flavoenzyme cholesterol oxidase, SCOA (Streptomyces sp.SA-COO) has been determined to 0.95 A resolution. The large size (55kDa) and the high-resolution diffraction of this protein provides a unique opportunity to observe detailed electronic effects within a protein environment and to obtain a larger sampling for which to analyze these electronic and structural differences. It is well-known through spectroscopic methods that peptide carbonyl groups are polarized in alpha-helices. This electronic characteristic is evident in the sub-Angstrom electron density of SCOA. Our analysis indicates an increased tendency for the electron density of the main chain carbonyl groups within alpha-helices to be polarized toward the oxygen atoms. In contrast, the carbonyl groups in beta-sheet structures tend to exhibit a greater charge density between the carbon and oxygen atoms. Interestingly, the electronic differences observed at the carbonyl groups do not appear to be correlated to the bond distance of the peptide bond or the peptide planarity. This study gives important insight into the electronic effects of alpha-helix dipoles in enzymes and provides experimentally based observations that have not been previously characterized in protein structure.


    Organizational Affiliation

    Department of Molecular, Cellular and Developmental Biology, Sinsheimer Laboratory, University of California Santa Cruz, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cholesterol oxidase
A
504Streptomyces sp. (strain SA-COO)Gene Names: choA
EC: 5.3.3.1, 1.1.3.6
Find proteins for P12676 (Streptomyces sp. (strain SA-COO))
Go to UniProtKB:  P12676
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.119 
  • R-Value Work: 0.097 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.273α = 90.00
b = 72.964β = 105.18
c = 63.036γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
SHELXphasing
DENZOdata reduction
SHELXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-28
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance