SAXSdb — 2rkn

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

DIR1 protein

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 3 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8W453_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–77； UniProt 26–102

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	2rkn
Deposition date deposition_date	2007-10-17
Structure title title	X-ray structure of the self-defense and signaling protein DIR1 from Arabidopsis taliana
Keywords keywords	LTP, DEFENSE SIGNALING PROTEIN, SIGNALING PROTEIN, LIPID TRANSPORT; SIGNALING PROTEIN, LIPID TRANSPORT
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.

2rkn__assembly_1__model_1

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

Download this curve (.dat)

2rkn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rkn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	13.19 Å
Rg (electron density)	11.46 Å
Total Rg	12.91 Å
Atom count	620
Residues	77
Excluded volume	11231 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rkn__assembly_1__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	DIR1 protein
Molecular weight formula_weight	8050.1 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	852

AIDLCGMSQDELNECKPAVSKENPTSPSQPCCTALQHADFACLCGYKNSPWLGSFGVDPELASALPKQCGLANAPTC

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	pichia pastoris

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE
Molecular weight formula_weight	524.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2rknA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	110 — Hydrophobic Seed Protein
Homologous superfamily homologous superfamily	10 — Plant lipid-transfer and hydrophobic proteins

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Unit-cell length a length_a	28.655 Å
Unit-cell length b length_b	48.217 Å
Unit-cell length c length_c	54.406 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	9.920 Å
R factor r_factor	0.1920
R_work r_work	0.1890
R_free r_free	0.2520

X-ray structure of the self-defense and signaling protein DIR1 from Arabidopsis taliana

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

DIR1 protein

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

2rkn__assembly_1__model_1

2rkn__assembly_1__model_1 | I(q)

2rkn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (2)

X-ray structure of the self-defense and signaling protein DIR1 from Arabidopsis taliana

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

DIR1 protein

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

2rkn__assembly_1__model_1

2rkn__assembly_1__model_1 | I(q)

2rkn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (2)