9I4S | pdb_00009i4s

DtpB in complex with photocaged nitric oxide, 1.24 s, 64.4 microjoule, SSX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9I4S

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 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.

Macromolecule Content 

  • Total Structure Weight: 217.93 kDa 
  • Atom Count: 14,785 
  • Modeled Residue Count: 1,834 
  • Deposited Residue Count: 1,974 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dyp-type peroxidase family
A, B, C, D, E
A, B, C, D, E, F
329Streptomyces lividans 1326Mutation(s): 0 
Gene Names: SSPG_00656
UniProt
Find proteins for A0A7U9HFU5 (Streptomyces lividans 1326)
Explore A0A7U9HFU5 
Go to UniProtKB:  A0A7U9HFU5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7U9HFU5
Sequence Annotations
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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: 2.40 Å
  • R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.184α = 90
b = 123.175β = 90
c = 195.465γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
xia2data reduction
xia2data scaling
MOLREPphasing
Cootmodel building

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