9S5R image
Deposition Date 2025-07-29
Release Date 2026-06-10
Last Version Date 2026-06-10
Entry Detail
PDB ID:
9S5R
Keywords:
Title:
Time-resolved SFX series of the DtpAa Y389F variant mixed with hydrogen peroxide -time 5 s
Biological Source:
Source Organism(s):
Expression System(s):
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Free:
0.18
R-Value Work:
0.14
R-Value Observed:
0.15
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Deferrochelatase
Gene (Uniprot):SLI_2602
Chain IDs:A, B
Chain Length:373
Number of Molecules:2
Biological Source:Streptomyces lividans
Primary Citation

Abstact

The use of X-ray structures to determine and interpret the ferryl iron-oxygen bond order in molecular oxygen-activating heme enzymes has, in the past, been controversial. This has mainly stemmed from the susceptibility of ferryl species to X-ray-induced electronic state changes. In this work we establishe using time-resolved serial femtosecond X-ray crystallography (tr-SFX) on a dye-decolourising peroxidase that the ferryl intermediate species (Compounds I and II) captured following in situ mixing of microcrystals with H(2)O(2) have single, rather than the double bond character expected. X-ray emission validated tr-SFX data with quantum refinement, time-dependent-DFT calculations and QM/MM geometry optimizations together support the concept that the single iron-oxygen bond character is not an indication of ferryl reduction or a protonated form (Fe(IV)-OH) but is instead attributed to the existence of accessible excited states possessing ferric-oxyl (Fe(III)-O(*-)) character. Such states offer insight into the nature of ferryl heme.

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Primary Citation of related structures
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