SAXSdb — 2rd3

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

Transcriptional regulator

Helicobacter pylori

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O25874_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–223； UniProt 1–217 Author chain D； PDBConstruct 7–223； UniProt 1–217

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	2rd3
Deposition date deposition_date	2007-09-21
Structure title title	Crystal structure of TenA homologue (HP1287) from Helicobacter pylori
Keywords keywords	TenA, HP1287, Helicobacter pylori, Thiamin, Vitamin B1, thiaminase II, TRANSCRIPTION, 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.

2rd3__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2rd3__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rd3__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.73 Å
Rg (electron density)	24.79 Å
Total Rg	25.54 Å
Atom count	3542
Residues	436
Excluded volume	63266 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rd3__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2rd3__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2rd3__assembly_3__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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2rd3a1
Class class	a — All alpha proteins
Fold Fold fold	a.132 — Heme oxygenase-like
Superfamily Superfamily superfamily	a.132.1 — Heme oxygenase-like
Family Family family	a.132.1.0 — automated matches

Domain ID domain_id	d2rd3a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2rd3d1
Class class	a — All alpha proteins
Fold Fold fold	a.132 — Heme oxygenase-like
Superfamily Superfamily superfamily	a.132.1 — Heme oxygenase-like
Family Family family	a.132.1.0 — automated matches

Domain ID domain_id	d2rd3d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2rd3A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	910 — Heme Oxygenase; Chain A
Homologous superfamily homologous superfamily	10 — Heme oxygenase-like

Domain ID domain_id	2rd3D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	910 — Heme Oxygenase; Chain A
Homologous superfamily homologous superfamily	10 — Heme oxygenase-like

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Unit-cell length a length_a	148.420 Å
Unit-cell length b length_b	148.420 Å
Unit-cell length c length_c	233.525 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	32

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	125.000 Å
R factor r_factor	0.2364
R_work r_work	0.2353
R_free r_free	0.2576

Description description	Transcriptional regulator
Molecular weight formula_weight	25665.1 kDa
EC 编号 ec_number	3.5.99.2
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	3620

Crystal structure of TenA homologue (HP1287) from Helicobacter pylori

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

Transcriptional regulator

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

2rd3__assembly_3__model_1

2rd3__assembly_3__model_1 | I(q)

2rd3__assembly_3__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (5)

Source organism organism	Helicobacter pylori
Common name common_name	Campylobacter pylori
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	52

Crystal structure of TenA homologue (HP1287) from Helicobacter pylori

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

Transcriptional regulator

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

2rd3__assembly_3__model_1

2rd3__assembly_3__model_1 | I(q)

2rd3__assembly_3__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (5)