9HU1 | pdb_00009hu1

SSX structure of cytochrome c prime beta from Methylococcus capsulatus (Bath)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.237 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.196 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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
Cytochrome cA [auth B],
B [auth A]
137Methylococcus capsulatus str. BathMutation(s): 0 
Gene Names: ccpMCA2394
UniProt
Find proteins for G1UBD5 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore G1UBD5 
Go to UniProtKB:  G1UBD5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1UBD5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
C [auth B],
H [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth B],
G [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.227α = 90
b = 107.227β = 90
c = 107.227γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
xia2data reduction
xia2data scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

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