6I6G

Dehaloperoxidase B from Amphitrite ornata - complex with 5-bromoindole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography.

Moreno-Chicano, T.Ebrahim, A.Axford, D.Appleby, M.V.Beale, J.H.Chaplin, A.K.Duyvesteyn, H.M.E.Ghiladi, R.A.Owada, S.Sherrell, D.A.Strange, R.W.Sugimoto, H.Tono, K.Worrall, J.A.R.Owen, R.L.Hough, M.A.

(2019) IUCrJ 6: 1074-1085

  • DOI: https://doi.org/10.1107/S2052252519011655
  • Primary Citation of Related Structures:  
    6I6G, 6I7C, 6I7F, 6QWG

  • PubMed Abstract: 

    High-throughput X-ray crystal structures of protein-ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein-ligand complexes using SFX.


  • Organizational Affiliation

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


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: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61α = 90
b = 67.33β = 90
c = 68.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Data collection
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description