SAXSdb — 2d40

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

putative gentisate 1,2-dioxygenase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	FE (III) ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8X655_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–354； UniProt 1–342 Author chain B； PDBConstruct 13–354； UniProt 1–342 Author chain C； PDBConstruct 13–354； UniProt 1–342 Author chain D； PDBConstruct 13–354； UniProt 1–342

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	2d40
Deposition date deposition_date	2005-10-05
Structure title title	Crystal Structure of Z3393 from Escherichia coli O157:H7
Keywords keywords	;Gentisic Acid, 1, 2-dioxygenase, bicupin, tetramer, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, Structural Genomics, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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.

2d40__assembly_1__model_1

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

Download this curve (.dat)

2d40__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d40__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.85 Å
Rg (electron density)	31.86 Å
Total Rg	32.51 Å
Atom count	9063
Residues	1125
Excluded volume	159410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d40__assembly_1__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	putative gentisate 1,2-dioxygenase
Molecular weight formula_weight	40229.6 kDa
EC 编号 ec_number	1.13.11.4
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9579

MGSSHHHHHHGSMTDNNQNSREQFYQHISGQNLTPLWESLHHLVPKTPNANCAPAYWNYQEIRPLLLESGGLIGAKEAVRRVLVLENPALRGQSSITATLYAGLQLIMPGEVAPSHRHNQSALRFIVEGKGAFTAVDGERTPMNEGDFILTPQWRWHDHGNPGDEPVIWLDGLDLPLVNILGCGFAEDYPEEQQPVTRKEGDYLPRYAANMLPLRHQTGNSSPIFNYRYDRSREVLHDLTRLGDADEWDGYKMRYVNPVTGGYPMPSMGAFLQLLPKGFASRVARTTDSTIYHVVEGSGQVIIGNETFSFSAKDIFVVPTWHGVSFQTTQDSVLFSFSDRPVQEALGLFREARY

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	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	516

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2d40a1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.23 — Gentisate 1,2-dioxygenase-like

Domain ID domain_id	d2d40b_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.23 — Gentisate 1,2-dioxygenase-like

Domain ID domain_id	d2d40c_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.23 — Gentisate 1,2-dioxygenase-like

Domain ID domain_id	d2d40d_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.23 — Gentisate 1,2-dioxygenase-like

CATH v4.4 (4 domains)

Domain ID domain_id	2d40A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2d40B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2d40C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2d40D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

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Unit-cell length a length_a	54.134 Å
Unit-cell length b length_b	76.075 Å
Unit-cell length c length_c	85.464 Å
Unit-cell angle α angle_alpha	114.08 °
Unit-cell angle β angle_beta	94.93 °
Unit-cell angle γ angle_gamma	108.11 °
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	2.410 Å
Low-resolution limit resolution_low	34.500 Å
R factor r_factor	0.1772
R_work r_work	0.1734
R_free r_free	0.2494

Crystal Structure of Z3393 from Escherichia coli O157:H7

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

putative gentisate 1,2-dioxygenase

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

2d40__assembly_1__model_1

2d40__assembly_1__model_1 | I(q)

2d40__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Z3393 from Escherichia coli O157:H7

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

putative gentisate 1,2-dioxygenase

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

2d40__assembly_1__model_1

2d40__assembly_1__model_1 | I(q)

2d40__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)