3e4d

Structural and Kinetic Study of an S-Formylglutathione Hydrolase from Agrobacterium tumefaciens

Method: X-RAY DIFFRACTION

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

Esterase D

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	MAGNESIUM ION × 2 CHLORIDE ION × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 CHLORIDE ION × 4 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 CHLORIDE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A9CJ11_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–278； UniProt 1–277 Author chain B； PDBConstruct 2–278； UniProt 1–277 Author chain C； PDBConstruct 2–278； UniProt 1–277 Author chain D； PDBConstruct 2–278； UniProt 1–277 Author chain E； PDBConstruct 2–278； UniProt 1–277 Author chain F； PDBConstruct 2–278； UniProt 1–277

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	3e4d
Deposition date deposition_date	2008-08-11
Structure title title	Structural and Kinetic Study of an S-Formylglutathione Hydrolase from Agrobacterium tumefaciens
Keywords keywords	S-Formylglutathione Hydrolase, Hydrolase fold family, catalytic triad, kinetics, proposed reaction mechanism, HYDROLASE; HYDROLASE
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.

3e4d__assembly_2__model_1

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

Download this curve (.dat)

3e4d__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e4d__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.22 Å
Rg (electron density)	25.40 Å
Total Rg	25.95 Å
Atom count	4410
Residues	531
Excluded volume	78100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e4d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3e4d__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3e4d__assembly_3__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	Esterase D
Molecular weight formula_weight	31924.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,E,D,F
Atom count atom_count	13914

GMNIISQNTAFGGMQGVFSHQSETLKSEMTFAVYVPPKAIHEPCPVVWYLSGLTCTHANVMEKGEYRRMASELGLVVVCPDTSPRGNDVPDELTNWQMGKGAGFYLDATEEPWSEHYQMYSYVTEELPALIGQHFRADMSRQSIFGHSMGGHGAMTIALKNPERFKSCSAFAPIVAPSSADWSEPALEKYLGADRAAWRRYDACSLVEDGARFPEFLIDQGKADSFLEKGLRPWLFEEAIKGTDIGLTLRMHDRYDHSYYFISTFMDDHLKWHAERLG

Source Source

Source organism organism	Agrobacterium tumefaciens
NCBI taxonomy ID ncbi_taxonomy_id	176299
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	670

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3e4da1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3e4da2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e4db1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3e4db2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e4dc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3e4dc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e4dd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3e4de1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3e4de2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3e4df_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	3e4dA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3e4dB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3e4dC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3e4dD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3e4dE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3e4dF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	68.433 Å
Unit-cell length b length_b	68.949 Å
Unit-cell length c length_c	95.648 Å
Unit-cell angle α angle_alpha	92.41 °
Unit-cell angle β angle_beta	99.79 °
Unit-cell angle γ angle_gamma	98.47 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1830
R_work r_work	0.1810
R_free r_free	0.2190

Structural and Kinetic Study of an S-Formylglutathione Hydrolase from Agrobacterium tumefaciens

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

Esterase D

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

3e4d__assembly_2__model_1

3e4d__assembly_2__model_1 | I(q)

3e4d__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 (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) 16 domains

SCOP 2.08 (10 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structural and Kinetic Study of an S-Formylglutathione Hydrolase from Agrobacterium tumefaciens

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

Esterase D

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

3e4d__assembly_2__model_1

3e4d__assembly_2__model_1 | I(q)

3e4d__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 (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) 16 domains

SCOP 2.08 (10 domains)

CATH v4.4 (6 domains)

7. Citations (1)