SAXSdb — 1tdt

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

TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE

Mycobacterium bovis

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_MYCBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–259； UniProt 1–259 Author chain B； PDBConstruct 1–259； UniProt 1–259 Author chain C； PDBConstruct 1–259； UniProt 1–259

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	1tdt
Deposition date deposition_date	1996-11-19
Structure title title	THREE-DIMENSIONAL STRUCTURE OF TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE
Keywords keywords	TRANSFERASE, SUCCINYLTRANSFERASE, LYSINE METABOLISM, HEXAPEPTIDE TRANSFERASE, CELL WALL BIOSYNTHESIS; 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.

1tdt__assembly_1__model_1

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

Download this curve (.dat)

1tdt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tdt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.31 Å
Rg (electron density)	26.05 Å
Total Rg	26.86 Å
Atom count	5780
Residues	764
Excluded volume	102530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tdt__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) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1tdta_
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	d1tdtb_
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	d1tdtc_
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 (6 domains)

Domain ID domain_id	1tdtA01
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	1tdtA02
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

Domain ID domain_id	1tdtB01
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	1tdtB02
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

Domain ID domain_id	1tdtC01
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	1tdtC02
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	60.600 Å
Unit-cell length b length_b	107.900 Å
Unit-cell length c length_c	70.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	0.1700
R_free r_free	0.2300

Description description	TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE
Molecular weight formula_weight	28249.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5995

THREE-DIMENSIONAL STRUCTURE OF TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE

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

TETRAHYDRODIPICOLINATE-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

1tdt__assembly_1__model_1

1tdt__assembly_1__model_1 | I(q)

1tdt__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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (2)

Source organism organism	Mycobacterium bovis
NCBI taxonomy ID ncbi_taxonomy_id	1765
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	215

THREE-DIMENSIONAL STRUCTURE OF TETRAHYDRODIPICOLINATE-N-SUCCINYLTRANSFERASE

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

TETRAHYDRODIPICOLINATE-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

1tdt__assembly_1__model_1

1tdt__assembly_1__model_1 | I(q)

1tdt__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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (2)