SAXSdb — 2ycd

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

GLUTATHIONE S-TRANSFERASE

AGROBACTERIUM TUMEFACIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	S-(P-NITROBENZYL)GLUTATHIONE × 2 PHOSPHATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A9CFJ9_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–230； UniProt 1–230

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	2ycd
Deposition date deposition_date	2011-03-13
Structure title title	Structure of a novel Glutathione Transferase from Agrobacterium tumefaciens.
Keywords keywords	TRANSFERASE, SOIL BACTERIA, HERBICIDE DETOXIFICATION; TRANSFERASE
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.

2ycd__assembly_1__model_1

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

Download this curve (.dat)

2ycd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ycd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.19 Å
Rg (electron density)	20.79 Å
Total Rg	21.65 Å
Atom count	3476
Residues	426
Excluded volume	61604 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ycd__assembly_1__model_1`	dimeric （2）	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	GLUTATHIONE S-TRANSFERASE
Molecular weight formula_weight	26172.9 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	2105

MSNIETVPASIEMKPNPTITVFERSPDGGRGLARDMPVRWALEEVGQPYHVRRLSFEAMKEASHLAYQPFGQIPSYEQGDLILFESGAIVMHIAQHHSGLLPEDQLRRARTVAWMFAALNTIEPSILNFTTVWLFERNEPWHEARLARTKEQLLKRLDELSAWLGDREWLEGSFSAADILMICVLRRLESSGILKDYGNLLAYVERGKARPAFKRAFDAQLAVFTAASKN

Source Source

Source organism organism	AGROBACTERIUM TUMEFACIENS
NCBI taxonomy ID ncbi_taxonomy_id	358
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	S-(P-NITROBENZYL)GLUTATHIONE
Molecular weight formula_weight	442.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	313

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2ycdA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	2ycdA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	49.200 Å
Unit-cell length b length_b	95.500 Å
Unit-cell length c length_c	88.100 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	19.766 Å
R factor r_factor	0.1732
R_work r_work	0.1725
R_free r_free	0.1865

Structure of a novel Glutathione Transferase from Agrobacterium tumefaciens.

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

GLUTATHIONE S-TRANSFERASE

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

2ycd__assembly_1__model_1

2ycd__assembly_1__model_1 | I(q)

2ycd__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of a novel Glutathione Transferase from Agrobacterium tumefaciens.

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

GLUTATHIONE S-TRANSFERASE

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

2ycd__assembly_1__model_1

2ycd__assembly_1__model_1 | I(q)

2ycd__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 (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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)