SAXSdb — 2gok

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

Imidazolonepropionase

Agrobacterium tumefaciens str.

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 MAGNESIUM ION × 2 CHLORIDE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HUTI_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–421； UniProt 2–419 Author chain B； PDBConstruct 4–421； UniProt 2–419

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	2gok
Deposition date deposition_date	2006-04-13
Structure title title	Crystal structure of the imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution
Keywords keywords	;9252b, Imidazolonepropionase, Protein Structure Initiative II (PSI-II), Histidine metabolism, Structural Genomics, New York SGX Research Center for Structural Genomics, NYSGXRC, 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.

2gok__assembly_1__model_1

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

Download this curve (.dat)

2gok__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gok__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.49 Å
Rg (electron density)	27.34 Å
Total Rg	28.04 Å
Atom count	6053
Residues	808
Excluded volume	107790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gok__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 (6)

Entity 1 Entity 1 polymer

Description description	Imidazolonepropionase
Molecular weight formula_weight	45660.6 kDa
EC 编号 ec_number	3.5.2.7
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	6549

MSLPGNNSAKGTATGNATALWRNAQLATLNPAMDGIGAVENAVIAVRNGRIAFAGPESDLPDDLSTADETTDCGGRWITPALIDCHTHLVFGGNRAMEFEMRLNGATYEEIAKAGGGIVSSVRDTRALSDEVLVAQALPRLDTLLSEGVSTIEIKSGYGLDIETELKMLRVARRLETLRPVRIVTSYLAAHATPADYKGRNADYITDVVLPGLEKAHAEGLADAVDGFCEGIAFSVKEIDRVFAAAQQRGLPVKLHAEQLSNLGGAELAASYNALSADHLEYLDETGAKALAKAGTVAVLLPGAFYALREKQLPPVQALRDAGAEIALATDCNPGTSPLTSLLLTMNMGATLFRMTVEECLTATTRNAAKALGLLAETGTLEAGKSADFAIWDIERPAELVYRIGFNPLHARIFKGQKVSPEGHHHHHH

Source Source

Source organism organism	Agrobacterium tumefaciens str.
NCBI taxonomy ID ncbi_taxonomy_id	176299
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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	496

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2goka1
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.92.1.10 — Imidazolonepropionase-like

Domain ID domain_id	d2goka2
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.1.9.17 — Imidazolonepropionase-like

Domain ID domain_id	d2gokb1
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.92.1.10 — Imidazolonepropionase-like

Domain ID domain_id	d2gokb2
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.1.9.17 — Imidazolonepropionase-like

CATH v4.4 (4 domains)

Domain ID domain_id	2gokA01
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	2gokA02
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	2gokB01
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	2gokB02
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	140.754 Å
Unit-cell length b length_b	63.630 Å
Unit-cell length c length_c	103.716 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.93 °
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	1.870 Å
Low-resolution limit resolution_low	23.640 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2310

Crystal structure of the imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution

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

Imidazolonepropionase

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

2gok__assembly_1__model_1

2gok__assembly_1__model_1 | I(q)

2gok__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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)

Crystal structure of the imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution

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

Imidazolonepropionase

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

2gok__assembly_1__model_1

2gok__assembly_1__model_1 | I(q)

2gok__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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)