SAXSdb — 2vy2

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN LEAFY

ARABIDOPSIS THALIANA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;5'-D(APTPTPTPAPAPTPCPCPAP APTPGPGPTPTPAPCPAPA)-3' ; × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LFY_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–194； UniProt 231–424

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2vy2
Deposition date deposition_date	2008-07-16
Structure title title	Structure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AG-I promoter
Keywords keywords	;DNA-BINDING, POLYMORPHISM, TRANSCRIPTION, DEVELOPMENTAL PROTEIN TRANSCRIPTION REGULATION, HOMEOTIC GENES, ACTIVATOR, DIFFERENTIATION FLOWER DEVELOPMENT, FLOWERING, COILED COIL GENES ;; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2vy2__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2vy2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vy2__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	26.11 Å
Rg (electron density)	25.54 Å
Total Rg	26.16 Å
Atom count	3458
Residues	366
Excluded volume	58698 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vy2__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN LEAFY
Molecular weight formula_weight	21892.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1954

LGTERQREHPFIVTEPGEVARGKKNGLDYLFHLYEQCREFLLQVQTIAKDRGEKCPTKVTNQVFRYAKKSGASYINKPKMRHYVHCYALHCLDEEASNALRRAFKERGENVGSWRQACYKPLVNIACRHGWDIDAVFNAHPRLSIWYVPTKLRQLCHLERNNAVAAAAALVGGISCTGSSTSGRGGCGGDDLRF

Source Source

Source organism organism	ARABIDOPSIS THALIANA
Common name common_name	MOUSE-EAR CRESS
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	;5'-D(APTPTPTPAPAPTPCPCPAP APTPGPGPTPTPAPCPAPA)-3' ;
Molecular weight formula_weight	6116.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	W

ATTTAATCCAATGGTTACAA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	46

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2vy2A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4180 — Protein LEAFY
Homologous superfamily homologous superfamily	10 — Protein LEAFY

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Unit-cell length a length_a	98.850 Å
Unit-cell length b length_b	98.850 Å
Unit-cell length c length_c	177.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.951 Å
R factor r_factor	0.2315
R_work r_work	0.2300
R_free r_free	0.2619

Structure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AG-I promoter

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN LEAFY

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2vy2__assembly_1__model_1

2vy2__assembly_1__model_1 | I(q)

2vy2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AG-I promoter

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN LEAFY

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2vy2__assembly_1__model_1

2vy2__assembly_1__model_1 | I(q)

2vy2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)