9FWY | pdb_00009fwy

Structure of the Nothoceros aenigmaticus LFY DNA-binding domain bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb9FWY/pdb
• NAKB: 9FWY

• Classification: DNA BINDING PROTEIN
• Organism(s): Nothoceros aenigmaticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-01 Released: 2025-07-09 
• Deposition Author(s): Verhage, L., Zubieta, C., Nanao, M.H., Parcy, F.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.297 (Depositor), 0.313 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.274 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

Structure of the Nothoceros aenigmaticus LFY DNA-binding domain bound to DNA

Verhage, L., Zubieta, C., Nanao, M.H., Dumas, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.01 kDa 
• Atom Count: 3,812 
• Modeled Residue Count: 377 
• Deposited Residue Count: 396 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Floricaula/leafy-like transcription factor	A, B	169	Nothoceros aenigmaticus	Mutation(s): 0
UniProt
Find proteins for W8EDT4 (Nothoceros aenigmaticus) Explore W8EDT4  Go to UniProtKB:  W8EDT4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (29-MER)	C [auth F]	29	Nothoceros aenigmaticus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (29-MER)	D [auth G]	29	Nothoceros aenigmaticus

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.297 (Depositor), 0.313 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.274 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.22	α = 90
b = 90.9	β = 90
c = 152.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Verhage, L., Zubieta, C., Nanao, M.H., Parcy, F.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release