9HL1 | pdb_00009hl1

DtpB in complex with photocaged nitric oxide, 10 ms, 10 microjoule, SFX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.234 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Time-resolved serial synchrotron and serial femtosecond crystallography of heme proteins using photocaged nitric oxide.

Smyth, P.Jaho, S.Williams, L.J.Karras, G.Fitzpatrick, A.Thompson, A.J.Battah, S.Axford, D.Horrell, S.Lucic, M.Ishihara, K.Kataoka, M.Matsuura, H.Shimba, K.Tono, K.Tosha, T.Sugimoto, H.Owada, S.Hough, M.A.Worrall, J.A.R.Owen, R.L.

(2025) IUCrJ 12: 582-594

  • DOI: https://doi.org/10.1107/S2052252525006645
  • Primary Citation of Related Structures:  
    9HL1, 9HO7, 9HQT, 9HS8, 9HTC, 9HTT, 9HTV, 9HU1, 9HXX, 9HYV, 9HYZ, 9I4Q, 9I4S, 9I4U, 9I6G, 9IA9, 9IAA, 9Q86, 9QME

  • PubMed Abstract: 

    Time-resolved X-ray crystallography is undergoing a renaissance due to the development of serial crystallography at synchrotron and XFEL beamlines. Crucial to such experiments are efficient and effective methods for uniformly initiating time-dependent processes within microcrystals, such as ligand binding, enzymatic reactions or signalling. A widely applicable approach is the use of photocaged substrates, where the photocage is soaked into the crystal in advance and then activated using a laser pulse to provide uniform initiation of the reaction throughout the crystal. This work characterizes photocage release of nitric oxide and binding of this ligand to two heme protein systems, cytochrome c'-β and dye-decolourizing peroxidase B using a fixed target sample delivery system. Laser parameters for photoactivation are systematically explored, and time-resolved structures over timescales ranging from 100 µs to 1.4 s using synchrotron and XFEL beamlines are described. The effective use of this photocage for time-resolved crystallography is demonstrated and appropriate illumination conditions for such experiments are determined.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dyp-type peroxidase family
A, B, C, D, E
A, B, C, D, E, F
306Streptomyces lividansMutation(s): 0 
Gene Names: SSPG_00656
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NO (Subject of Investigation/LOI)
Query on NO

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.234 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.073α = 90
b = 122.875β = 90
c = 194.936γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references