SAXSdb — 3cqr

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

Violaxanthin de-epoxidase, chloroplast

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GADOLINIUM ATOM × 3 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GADOLINIUM ATOM × 3 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	GADOLINIUM ATOM × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VDE_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–177； UniProt 191–366 Author chain B； PDBConstruct 2–177； UniProt 191–366

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	3cqr
Deposition date deposition_date	2008-04-03
Structure title title	Crystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH5
Keywords keywords	;Lipocalin, Enzyme, de-epoxidase, Xanthophyll cycle, non photochemical quenching, NPQ, Violaxanthin, Antheraxanthin, Zeaxanthin, Chloroplast, Membrane, Oxidoreductase, Thylakoid, Transit peptide ;; OXIDOREDUCTASE
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.

3cqr__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3cqr__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cqr__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.10 Å
Rg (electron density)	24.54 Å
Total Rg	25.40 Å
Atom count	2776
Residues	341
Excluded volume	48797 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cqr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cqr__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3cqr__assembly_3__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	Violaxanthin de-epoxidase, chloroplast
Molecular weight formula_weight	21343.5 kDa
EC 编号 ec_number	1.10.99.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2979

MDLGEFPAPDPSVLVQNFNISDFNGKWYITSGLNPTFDAFDCQLHEFHTEGDNKLVGNISWRIKTLDSGFFTRSAVQKFVQDPNQPGVLYNHDNEYLHYQDDWYILSSKIENKPEDYIFVYYRGRNDAWDGYGGAVVYTRSSVLPNSIIPELEKAAKSIGRDFSTFIRTDNTCGPEPRSHHHHHH

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 non-polymer

Description description	GADOLINIUM ATOM
Molecular weight formula_weight	157.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3cqrA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	3cqrB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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Unit-cell length a length_a	122.297 Å
Unit-cell length b length_b	122.297 Å
Unit-cell length c length_c	158.337 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	32

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.200 Å
R factor r_factor	0.2090
R_work r_work	0.2080
R_free r_free	0.2340

Crystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH5

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

Violaxanthin de-epoxidase, chloroplast

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

3cqr__assembly_2__model_1

3cqr__assembly_2__model_1 | I(q)

3cqr__assembly_2__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of the Lipocalin domain of Violaxanthin de-epoxidase (VDE) at pH5

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

Violaxanthin de-epoxidase, chloroplast

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

3cqr__assembly_2__model_1

3cqr__assembly_2__model_1 | I(q)

3cqr__assembly_2__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)