9KK7 | pdb_00009kk7

Neutron structure of Ferredoxin-NADP+ reductase from maize root -Reduced form


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.246 (Depositor) 
  • R-Value Work: 
    0.197 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Redox-dependent hydrogen-bond network rearrangement of ferredoxin-NADP + reductase revealed by high-resolution X-ray and neutron crystallography.

Uenaka, M.Ohnishi, Y.Ise, A.Yu, J.Yano, N.Kusaka, K.Tanaka, H.Kurisu, G.

(2025) Acta Crystallogr F Struct Biol Commun 81: 73-84

  • DOI: https://doi.org/10.1107/S2053230X25000524
  • Primary Citation of Related Structures:  
    9KK7, 9KKC, 9KKG, 9KKH, 9L8G

  • PubMed Abstract: 

    High-resolution X-ray and neutron crystallography were employed to elucidate redox-dependent structural changes in ferredoxin-NADP + reductase (FNR) from maize. This study focused on the rearrangement of hydrogen-bond networks upon FAD reduction. The X-ray structures of wild-type FNR in oxidized and reduced states were refined to 1.15 and 1.10 Å resolution, respectively, revealing no large structural changes in the main-chain backbones. Neutron crystallography provided complementary insights, confirming protonation at N1 and N5 of the isoalloxazine ring and visualizing hydrogen bonds that were undetectable by X-ray analysis. These findings illuminate the dynamic reorganization of water-mediated hydrogen-bond networks during redox transitions, which may underpin the redox-dependent modulation of partner binding by FNR. This integrated structural approach highlights the synergistic use of X-ray and neutron crystallography in studying redox-active proteins.


  • Organizational Affiliation

    Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin--NADP reductase, chloroplastic309Zea maysMutation(s): 0 
Gene Names: 542713ZEAMMB73_Zm00001d034345
EC: 1.18.1.2
UniProt
Find proteins for B4G043 (Zea mays)
Explore B4G043 
Go to UniProtKB:  B4G043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4G043
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.246 (Depositor) 
  • R-Value Work:  0.197 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.32α = 90
b = 59.32β = 90
c = 187.69γ = 120
Software Package:
Software NamePurpose
STARGazerdata reduction
STARGazerdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJSP2138

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Database references
  • Version 1.2: 2025-03-12
    Changes: Database references