7KCU

Joint neutron/X-ray structure of Oxyferrous Dehaloperoxidase B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.160 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.255 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature.

Moreno-Chicano, T.Carey, L.M.Axford, D.Beale, J.H.Doak, R.B.Duyvesteyn, H.M.E.Ebrahim, A.Henning, R.W.Monteiro, D.C.F.Myles, D.A.Owada, S.Sherrell, D.A.Straw, M.L.Srajer, V.Sugimoto, H.Tono, K.Tosha, T.Tews, I.Trebbin, M.Strange, R.W.Weiss, K.L.Worrall, J.A.R.Meilleur, F.Owen, R.L.Ghiladi, R.A.Hough, M.A.

(2022) IUCrJ 9: 610-624

  • DOI: https://doi.org/10.1107/S2052252522006418
  • Primary Citation of Related Structures:  
    7ADQ, 7JOR, 7KCU, 7KFM

  • PubMed Abstract: 

    Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.


  • Organizational Affiliation

    School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehaloperoxidase B
A, B
137Amphitrite ornataMutation(s): 0 
UniProt
Find proteins for Q9NAV7 (Amphitrite ornata)
Explore Q9NAV7 
Go to UniProtKB:  Q9NAV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NAV7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.83α = 90
b = 67.1β = 90
c = 69.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
SCALAdata scaling
LAUEGENdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1150709

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description