SAXSdb — 1onx

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

Isoaspartyl dipeptidase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	ZINC ION × 16 ASPARTIC ACID × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IADA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–390； UniProt 1–390 Author chain B； PDBConstruct 1–390； UniProt 1–390

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	1onx
Deposition date deposition_date	2003-03-02
Structure title title	Crystal structure of isoaspartyl dipeptidase from escherichia coli complexed with aspartate
Keywords keywords	amidohydrolase, hydrolase, metalloprotease; 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.

1onx__assembly_1__model_1

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

Download this curve (.dat)

1onx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1onx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.51 Å
Rg (electron density)	43.19 Å
Total Rg	43.53 Å
Atom count	23152
Residues	3104
Excluded volume	413260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1onx__assembly_1__model_1`	octameric （8）	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	Isoaspartyl dipeptidase
Molecular weight formula_weight	41167.8 kDa
EC 编号 ec_number	3.4.19.-
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	6053

MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVKCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFETA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

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	4

Entity 3 Entity 3 non-polymer

Description description	ASPARTIC ACID
Molecular weight formula_weight	133.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	257

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1onxa1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.7 — Isoaspartyl dipeptidase

Domain ID domain_id	d1onxa2
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.1.9.13 — Isoaspartyl dipeptidase, catalytic domain

Domain ID domain_id	d1onxb1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.7 — Isoaspartyl dipeptidase

Domain ID domain_id	d1onxb2
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.1.9.13 — Isoaspartyl dipeptidase, catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	1onxA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1onxA02
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	1onxB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1onxB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

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Unit-cell length a length_a	119.100 Å
Unit-cell length b length_b	119.100 Å
Unit-cell length c length_c	138.100 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	16

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1820
R_work r_work	0.1770
R_free r_free	0.2460

Crystal structure of isoaspartyl dipeptidase from escherichia coli complexed with aspartate

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

Isoaspartyl dipeptidase

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

1onx__assembly_1__model_1

1onx__assembly_1__model_1 | I(q)

1onx__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of isoaspartyl dipeptidase from escherichia coli complexed with aspartate

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

Isoaspartyl dipeptidase

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

1onx__assembly_1__model_1

1onx__assembly_1__model_1 | I(q)

1onx__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)