Dye type peroxidase Aa from Streptomyces lividans: 164 kGy structure

Experimental Data Snapshot

  • Resolution: 1.98 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins.

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

(2019) IUCrJ 6: 543-551

  • DOI: https://doi.org/10.1107/S2052252519003956
  • Primary Citation of Related Structures:  
    6I43, 6I7Z, 6I8E, 6I8I, 6I8J, 6I8K, 6I8O, 6I8P, 6I8Q, 6IBN, 6Q31, 6Q34, 6Q3D, 6Q3E

  • PubMed Abstract: 

    An approach is demonstrated to obtain, in a sample- and time-efficient manner, multiple dose-resolved crystal structures from room-temperature protein microcrystals using identical fixed-target supports at both synchrotrons and X-ray free-electron lasers (XFELs). This approach allows direct comparison of dose-resolved serial synchrotron and damage-free XFEL serial femtosecond crystallography structures of radiation-sensitive proteins. Specifically, serial synchrotron structures of a heme peroxidase enzyme reveal that X-ray induced changes occur at far lower doses than those at which diffraction quality is compromised (the Garman limit), consistent with previous studies on the reduction of heme proteins by low X-ray doses. In these structures, a functionally relevant bond length is shown to vary rapidly as a function of absorbed dose, with all room-temperature synchrotron structures exhibiting linear deformation of the active site compared with the XFEL structure. It is demonstrated that extrapolation of dose-dependent synchrotron structures to zero dose can closely approximate the damage-free XFEL structure. This approach is widely applicable to any protein where the crystal structure is altered by the synchrotron X-ray beam and provides a solution to the urgent requirement to determine intact structures of such proteins in a high-throughput and accessible manner.

  • Organizational Affiliation

    RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
362Streptomyces lividans TK24Mutation(s): 0 
Gene Names: SLIV_26340
EC: 1.11.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C34 H32 Fe N4 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 1.98 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.008α = 90
b = 68.281β = 105.79
c = 74.917γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DIALSdata reduction
cctbx.primedata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description