9G19 | pdb_00009g19

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

PDB DOI: https://doi.org/10.2210/pdb9G19/pdb
NAKB: 9G19

Classification: GENE REGULATION
Organism(s): Nothoceros aenigmaticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-09 Released: 2025-07-16
Deposition Author(s): Zubieta, C., Verhage, L., Nanao, M.H., Parcy, F.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free:
0.303 (Depositor), 0.303 (DCC)
R-Value Work:
0.243 (Depositor), 0.243 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

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

Zubieta, C., Verhage, L., Nanao, M.H., Parcy, F.

To be published.

Macromolecule Content

Total Structure Weight: 54.25 kDa
Atom Count: 3,456
Modeled Residue Count: 360
Deposited Residue Count: 386
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Floricaula/leafy-like transcription factor	A, B	168	Nothoceros aenigmaticus	Mutation(s): 0
UniProt
Find proteins for W8EDT4 (Nothoceros aenigmaticus) Explore W8EDT4 Go to UniProtKB: W8EDT4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8EDT4
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (25-MER)	C	25	Nothoceros aenigmaticus
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA (25-MER)	D	25	Nothoceros aenigmaticus
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free: 0.303 (Depositor), 0.303 (DCC)
R-Value Work: 0.243 (Depositor), 0.243 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.708	α = 90
b = 154.104	β = 90
c = 53.062	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.