2orm

Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue DmpI from Helicobacter pylori.

Method: X-RAY DIFFRACTION

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

Probable tautomerase HP0924

Helicobacter pylori

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y924_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–67； UniProt 2–68 Author chain B； PDBConstruct 1–67； UniProt 2–68 Author chain C； PDBConstruct 1–67； UniProt 2–68 Author chain D； PDBConstruct 1–67； UniProt 2–68 Author chain E； PDBConstruct 1–67； UniProt 2–68 Author chain F； PDBConstruct 1–67； UniProt 2–68

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	2orm
Deposition date deposition_date	2007-02-03
Structure title title	Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue DmpI from Helicobacter pylori.
Keywords keywords	homohexamer, 4-OT, 4-Oxalocrotonate Tautomerase Homologue, ISOMERASE; ISOMERASE
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.

2orm__assembly_1__model_1

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

Download this curve (.dat)

2orm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2orm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.84 Å
Rg (electron density)	20.09 Å
Total Rg	21.01 Å
Atom count	2932
Residues	393
Excluded volume	52412 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2orm__assembly_1__model_1`	hexameric （6）	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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2orma_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.0 — automated matches

Domain ID domain_id	d2ormb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.0 — automated matches

Domain ID domain_id	d2ormc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.0 — automated matches

Domain ID domain_id	d2ormd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.0 — automated matches

Domain ID domain_id	d2orme_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.0 — automated matches

Domain ID domain_id	d2ormf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2ormA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	2ormB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	2ormC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	2ormD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	2ormE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	2ormF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

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Unit-cell length a length_a	41.830 Å
Unit-cell length b length_b	50.770 Å
Unit-cell length c length_c	89.310 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	24.500 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2490

Description description	Probable tautomerase HP0924
Molecular weight formula_weight	7389.4 kDa
EC 编号 ec_number	5.3.2.-
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	3058

Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue DmpI from Helicobacter pylori.

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

Probable tautomerase HP0924

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

2orm__assembly_1__model_1

2orm__assembly_1__model_1 | I(q)

2orm__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Helicobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	85963
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	126

Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue DmpI from Helicobacter pylori.

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

Probable tautomerase HP0924

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

2orm__assembly_1__model_1

2orm__assembly_1__model_1 | I(q)

2orm__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)