4REK

Crystal structure and charge density studies of cholesterol oxidase from Brevibacterium sterolicum at 0.74 ultra-high resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.74 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.113 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.

Zarychta, B.Lyubimov, A.Ahmed, M.Munshi, P.Guillot, B.Vrielink, A.Jelsch, C.

(2015) Acta Crystallogr.,Sect.D 71: 954-968

  • DOI: 10.1107/S1399004715002382

  • PubMed Abstract: 
  • Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiatio ...

    Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.


    Organizational Affiliation

    Laboratoire de Cristallographie, Résonance Magnétique et Modélisations (CRM2), CNRS, UMR 7036, Institut Jean Barriol, Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, 54506 Vandoeuvre-lès-Nancy CEDEX, France.,Howard Hughes Medical Institute, Stanford, CA 94305-5432, USA.,School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cholesterol oxidase
A
499Streptomyces sp. (strain SA-COO)Mutation(s): 0 
Gene Names: choA
EC: 1.1.3.6
Find proteins for P12676 (Streptomyces sp. (strain SA-COO))
Go to UniProtKB:  P12676
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.74 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.113 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.240α = 90.00
b = 72.920β = 105.13
c = 63.010γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
Blu-Icedata collection
PHENIXrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description