SAXSdb — 2q4a

▼

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

Clavaminate synthase-like protein At3g21360

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	FE (III) ION × 2 SULFATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y3136_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–330； UniProt 1–330 Author chain B； PDBConstruct 1–330； UniProt 1–330

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2q4a
Deposition date deposition_date	2007-05-31
Structure title title	Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g21360
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, AT3G21360, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG, OXIDOREDUCTASE ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2q4a__assembly_1__model_4

Assembly 1 · Model 4 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2q4a__assembly_1__model_4 | I(q)

100 plotted points; both axes use logarithmic scales.

2q4a__assembly_1__model_4 | P(r) · Pending

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

Rg（Guinier）	28.94 Å
Rg (electron density)	28.28 Å
Total Rg	29.02 Å
Atom count	5163
Residues	643
Excluded volume	91771 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q4a__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2q4a__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2q4a__assembly_1__model_3`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2q4a__assembly_1__model_4`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Clavaminate synthase-like protein At3g21360
Molecular weight formula_weight	37260.4 kDa
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	23772

MAELLLVETPIPQQKHYESKPFPAVISPPSASIPIPALSLPLFTQTIKTQKHYLDSLLHESGAVLFRGFPVNSADDFNDVVEAFGFDELPYVGGAAPRTSVVGRVFTANESPPDQKIPFHHEMAQVREFPSKLFFYCEIEPKCGGETPIVLSHVVYERMKDKHPEFVQRLEEHGLLYVRVLGEDDDPSSPIGRGWKSTFLTHDKNLAEQRAVDLGMKLEWTEDGGAKTVMGPIPAIKYDESRNRKVWFNSMVAAYTGWEDKRNDPRKAVTFGDGKPLPADIVHDCLRILEEECVAVPWQRGDVLLIDNWAVLHSRRPFDPPRRVLASLCK

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	780

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2q4aa_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.8 — gamma-Butyrobetaine hydroxylase

Domain ID domain_id	d2q4ab_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.8 — gamma-Butyrobetaine hydroxylase

CATH v4.4 (2 domains)

Domain ID domain_id	2q4aA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	130 — Double-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Clavaminate synthase-like

Domain ID domain_id	2q4aB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	130 — Double-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Clavaminate synthase-like

▶

Unit-cell length a length_a	145.276 Å
Unit-cell length b length_b	61.094 Å
Unit-cell length c length_c	114.681 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	121.68 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.390 Å
Low-resolution limit resolution_low	43.630 Å
R factor r_factor	0.1710
R_work r_work	0.1710
R_free r_free	0.2350

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g21360

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

Clavaminate synthase-like protein At3g21360

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

2q4a__assembly_1__model_4

2q4a__assembly_1__model_4 | I(q)

2q4a__assembly_1__model_4 | 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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g21360

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

Clavaminate synthase-like protein At3g21360

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

2q4a__assembly_1__model_4

2q4a__assembly_1__model_4 | I(q)

2q4a__assembly_1__model_4 | 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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)