SAXSdb — 3bxy

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

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Escherichia coli

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DAPD_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–285； UniProt 2–274

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	3bxy
Deposition date deposition_date	2008-01-15
Structure title title	Crystal structure of tetrahydrodipicolinate N-succinyltransferase from E. coli
Keywords keywords	;left-handed beta-helix, Structural Genomics, CIHR, Canadian Institutes of Health Research, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, Acyltransferase, Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis, Transferase ;; TRANSFERASE
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.

3bxy__assembly_1__model_1

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

Download this curve (.dat)

3bxy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bxy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.96 Å
Rg (electron density)	26.60 Å
Total Rg	27.41 Å
Atom count	6342
Residues	825
Excluded volume	112480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bxy__assembly_1__model_1`	trimeric （3）	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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3bxya1
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.2 — Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD

Domain ID domain_id	d3bxya2
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	3bxyA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	166 — Tetrahydrodipicolinate-N-succinyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain

Domain ID domain_id	3bxyA02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

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Unit-cell length a length_a	102.924 Å
Unit-cell length b length_b	102.924 Å
Unit-cell length c length_c	69.229 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	44.590 Å
R factor r_factor	0.1760
R_work r_work	0.1750
R_free r_free	0.2055

Description description	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Molecular weight formula_weight	31114.2 kDa
EC 编号 ec_number	2.3.1.117
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2294

Crystal structure of tetrahydrodipicolinate N-succinyltransferase from E. coli

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

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

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

3bxy__assembly_1__model_1

3bxy__assembly_1__model_1 | I(q)

3bxy__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83334
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	175

Crystal structure of tetrahydrodipicolinate N-succinyltransferase from E. coli

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

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

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

3bxy__assembly_1__model_1

3bxy__assembly_1__model_1 | I(q)

3bxy__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)