SAXSdb — 3eg4

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

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

Brucella suis

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
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DAPD_BRUSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–304； UniProt 1–284

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	3eg4
Deposition date deposition_date	2008-09-10
Structure title title	Crystal structure of 2,3,4,5-Tetrahydropyridine-2-carboxylate N-Succinyltransferase from Brucella melitensis biovar abortus 2308
Keywords keywords	;SSGCID, TRANSFERASE, N-SUCCINYL-TRANSFERASE, BETA HELIX, Acyltransferase, Amino-acid biosynthesis, Cytoplasm, Diaminopimelate biosynthesis, Lysine biosynthesis, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease ;; 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.

3eg4__assembly_1__model_1

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

Download this curve (.dat)

3eg4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3eg4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.88 Å
Rg (electron density)	26.60 Å
Total Rg	27.44 Å
Atom count	6306
Residues	837
Excluded volume	112310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3eg4__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3eg4__assembly_2__model_1`	monomeric （1）	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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3eg4a_
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

CATH v4.4 (2 domains)

Domain ID domain_id	3eg4A01
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	3eg4A02
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	67.808 Å
Unit-cell length b length_b	67.808 Å
Unit-cell length c length_c	154.830 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	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.870 Å
Low-resolution limit resolution_low	25.800 Å
R factor r_factor	0.1320
R_work r_work	0.1300
R_free r_free	0.1660

Description description	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Molecular weight formula_weight	33020.6 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	2364

Crystal structure of 2,3,4,5-Tetrahydropyridine-2-carboxylate N-Succinyltransferase from Brucella melitensis biovar abortus 2308

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

3eg4__assembly_1__model_1

3eg4__assembly_1__model_1 | I(q)

3eg4__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Brucella suis
NCBI taxonomy ID ncbi_taxonomy_id	29461
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	250

Crystal structure of 2,3,4,5-Tetrahydropyridine-2-carboxylate N-Succinyltransferase from Brucella melitensis biovar abortus 2308

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

3eg4__assembly_1__model_1

3eg4__assembly_1__model_1 | I(q)

3eg4__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)