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
  • Primary Citation of Related Structures:  
    1N1P

  • 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 observe detailed electronic effects within a protein environment and to obtain a larger sampling for which to analyze these electronic and structural differences ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cholesterol oxidaseA504Streptomyces sp.Mutation(s): 0 
Gene Names: choA
EC: 1.1.3.6 (PDB Primary Data), 5.3.3.1 (UniProt)
Find proteins for P12676 (Streptomyces sp. (strain SA-COO))
Explore P12676 
Go to UniProtKB:  P12676
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-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
b = 72.964β = 105.18
c = 63.036γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-28
    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