9GZ4 | pdb_00009gz4

FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 
    0.152 (Depositor), 0.152 (DCC) 
  • R-Value Work: 
    0.144 (Depositor), 0.143 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Cyanophenylalanine as an Infrared Probe for Iron-Sulfur Cluster Redox State in Multicenter Metalloenzymes.

Duan, Z.Wei, J.Carr, S.B.Ramirez, M.Evans, R.M.Ash, P.A.Rodriguez-Macia, P.Sachdeva, A.Vincent, K.A.

(2025) Chembiochem 26: e202500251-e202500251

  • DOI: https://doi.org/10.1002/cbic.202500251
  • Primary Citation of Related Structures:  
    9GYD, 9GYL, 9GYN, 9GYR, 9GYU, 9GZ0, 9GZ4, 9GZL

  • PubMed Abstract: 

    We demonstrate that the noncanonical amino acid, para-cyanophenylalanine (CNF), when incorporated into metalloproteins, functions as an infrared spectroscopic probe for the redox state of iron sulfur clusters, offering a strategy for determining electron occupancy in the electron transport chains of complex metalloenzymes. We observe a redshift of ≈ 1 - 2 cm-1 in the NC stretching frequency following reduction of spinach ferredoxin modified to contain CNF close to its [2Fe-2S] centre, and this shift is reversed on re-oxidation. We extend this to CNF positioned near to the proximal [4Fe-4S] cluster of the [FeFe] hydrogenase from Desulfovibrio desulfuricans. In combination with a distal [4Fe-4S] cluster and the [4Fe-4S] cluster of the active site 'H-cluster' ([4Fe-4S]H), the proximal cluster forms an electron relay connecting the active site to the surface of the protein. Again, we observe a reversible shift in wavenumber for CNF following cluster reduction in either apo-protein (containing the iron-sulfur clusters but lacking the active site) or holo-protein with intact active site, demonstrating general applicability of this approach to studying complex metalloenzymes.


  • Organizational Affiliation
    • University of Oxford Department of Chemistry, Department of Chemistry, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic [Fe] hydrogenase large subunit396Desulfovibrio desulfuricansMutation(s): 0 
Gene Names: hydADVU_1769
EC: 1.12.7.2
UniProt
Find proteins for P07598 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P07598 
Go to UniProtKB:  P07598
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07598
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic [Fe] hydrogenase small subunit88Desulfovibrio desulfuricansMutation(s): 0 
Gene Names: hydBDVU_1770
EC: 1.12.7.2
UniProt
Find proteins for P07603 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P07603 
Go to UniProtKB:  P07603
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07603
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4WW
Query on 4WW

Download Ideal Coordinates CCD File 
F [auth A]bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+)
C8 H6 Fe2 N2 O3 S2
POEKPSQXPZCVMK-UHFFFAOYSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
LI
Query on LI

Download Ideal Coordinates CCD File 
J [auth A]LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
4CF
Query on 4CF
A
L-PEPTIDE LINKINGC10 H10 N2 O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free:  0.152 (Depositor), 0.152 (DCC) 
  • R-Value Work:  0.144 (Depositor), 0.143 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.718α = 90
b = 87.713β = 90
c = 89.885γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R018413/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/X002624/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references
  • Version 1.2: 2025-07-30
    Changes: Database references