SAXSdb — 2o4m

▼

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

Parathion hydrolase

Brevundimonas diminuta

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 11 CACODYLATE ION × 2 ACETIC ACID × 2 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 12 CACODYLATE ION × 2 ACETIC ACID × 1 GLYCEROL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OPD_BREDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–331； UniProt 34–364 Author chain B； PDBConstruct 1–331； UniProt 34–364 Author chain C； PDBConstruct 1–331； UniProt 34–364 Author chain P； PDBConstruct 1–331； UniProt 34–364

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	2o4m
Deposition date deposition_date	2006-12-04
Structure title title	Structure of Phosphotriesterase mutant I106G/F132G/H257Y
Keywords keywords	METALLOENZYME, TIM BARREL, NERVE AGENTS, HYDROLASE; HYDROLASE
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.

2o4m__assembly_1__model_1

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

Download this curve (.dat)

2o4m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2o4m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.66 Å
Rg (electron density)	27.09 Å
Total Rg	27.91 Å
Atom count	5070
Residues	659
Excluded volume	90491 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2o4m__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2o4m__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Parathion hydrolase
Molecular weight formula_weight	35808.7 kDa
EC 编号 ec_number	3.1.8.1
Mutation mutation	I106G, F132G, H257Y
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,P
Atom count atom_count	11956

GDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDGGRDVSLLAEVSRAADVHIVAATGLWGDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPYSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLRA

Source Source

Source organism organism	Brevundimonas diminuta
NCBI taxonomy ID ncbi_taxonomy_id	293
Host organism host_organism	Escherichia coli BL21(DE3)

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	23

Entity 3 Entity 3 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1594

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2o4ma_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.3 — Phosphotriesterase-like

Domain ID domain_id	d2o4mb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.3 — Phosphotriesterase-like

Domain ID domain_id	d2o4mc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.3 — Phosphotriesterase-like

Domain ID domain_id	d2o4mp_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.3 — Phosphotriesterase-like

CATH v4.4 (4 domains)

Domain ID domain_id	2o4mA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	2o4mB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	2o4mC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	2o4mP00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

▶

Unit-cell length a length_a	56.759 Å
Unit-cell length b length_b	68.906 Å
Unit-cell length c length_c	89.670 Å
Unit-cell angle α angle_alpha	90.03 °
Unit-cell angle β angle_beta	100.29 °
Unit-cell angle γ angle_gamma	94.12 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.640 Å
Low-resolution limit resolution_low	28.330 Å
R factor r_factor	0.1920
R_work r_work	0.1890
R_free r_free	0.2440

Structure of Phosphotriesterase mutant I106G/F132G/H257Y

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

Parathion hydrolase

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

2o4m__assembly_1__model_1

2o4m__assembly_1__model_1 | I(q)

2o4m__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of Phosphotriesterase mutant I106G/F132G/H257Y

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

Parathion hydrolase

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

2o4m__assembly_1__model_1

2o4m__assembly_1__model_1 | I(q)

2o4m__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)