8S8Q | pdb_00008s8q

Structure of the Interfilum paradoxum LFY DNA-binding domain bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb8S8Q/pdb
• NAKB: 8S8Q

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


• Deposited: 2024-03-07 Released: 2025-03-19 
• Deposition Author(s): Verhage, L., Zubieta, C., Nanao, M.H.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.237 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structure of the Interfilum paradoxum LFY DNA-binding domain bound to DNA

Verhage, L., Zubieta, C., Nanao, M.H.

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 (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 52.18 kDa 
• Atom Count: 3,614 
• Modeled Residue Count: 370 
• Deposited Residue Count: 372 
• 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, C [auth B]	162	Interfilum paradoxum	Mutation(s): 0  Gene Names: KFL_007730030
UniProt
Find proteins for A0A1Y1IRK2 (Klebsormidium nitens) Explore A0A1Y1IRK2  Go to UniProtKB:  A0A1Y1IRK2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*TP*GP*CP*AP*GP*CP*GP*AP*CP*CP*GP*GP*TP*AP*GP*CP*AP*AP*CP*GP*CP*A)-3')	B [auth D]	24	Interfilum paradoxum

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*CP*GP*TP*TP*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*GP*CP*TP*GP*CP*AP*CP*T)-3')	D [auth C]	24	Interfilum paradoxum

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.237 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.89	α = 90
b = 144.89	β = 90
c = 69.836	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Verhage, L., Zubieta, C., Nanao, M.H.

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

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release