2gn0

Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 1.7 A resolution (Triclinic form with one complete subunit built in alternate conformation)

Method: X-RAY DIFFRACTION

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

Threonine dehydratase catabolic

Salmonella typhimurium

UniProt P11954

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THD2_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–342； UniProt 2–329 Author chain B； PDBConstruct 15–342； UniProt 2–329 Author chain C； PDBConstruct 15–342； UniProt 2–329 Author chain D； PDBConstruct 15–342； UniProt 2–329

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	2gn0
Deposition date deposition_date	2006-04-09
Structure title title	Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 1.7 A resolution (Triclinic form with one complete subunit built in alternate conformation)
Keywords keywords	TdcB, Biodegradative threonine deaminase, PLP, Threonine dehydratase, L-threonine metabolism, Alternate conformation, Lyase; LYASE
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.

2gn0__assembly_1__model_1

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

Download this curve (.dat)

2gn0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gn0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.68 Å
Rg (electron density)	25.75 Å
Total Rg	26.45 Å
Atom count	4829
Residues	645
Excluded volume	86331 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gn0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2gn0__assembly_1__model_2`	dimeric （2）	Excluded	—	—
	Exclusion reason： The polymer contains overlapping alternate coordinates, and a complete, coherent single conformation cannot be selected automatically.
2	1	`2gn0__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	2	`2gn0__assembly_2__model_2`	dimeric （2）	Excluded	—	—
	Exclusion reason： The polymer contains overlapping alternate coordinates, and a complete, coherent single conformation cannot be selected automatically.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Threonine dehydratase catabolic
Molecular weight formula_weight	36887.1 kDa
EC 编号 ec_number	4.3.1.19
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	20933

MRGSHHHHHHGMASHITYDLPVAIEDILEAKKRLAGKIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTEAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDNFNDTIAKVSEIVETEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGLIAGIAIAIKSINPTIKVIGVQAENVHGMAASYYTGEITTHRTTGTLADGCDVSRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVITEGAGALACAALLSGKLDSHIQNRKTVSIISGGNIDLSRVSQITGLVDA

Source Source

Source organism organism	Salmonella typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	602
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	780

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2gn0a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.0 — automated matches

Domain ID domain_id	d2gn0a2
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	d2gn0b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.0 — automated matches

Domain ID domain_id	d2gn0c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.0 — automated matches

Domain ID domain_id	d2gn0c2
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	d2gn0d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2gn0A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	2gn0A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	2gn0B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	2gn0B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	2gn0C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	2gn0C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	2gn0D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	2gn0D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

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Unit-cell length a length_a	56.675 Å
Unit-cell length b length_b	76.827 Å
Unit-cell length c length_c	78.501 Å
Unit-cell angle α angle_alpha	66.12 °
Unit-cell angle β angle_beta	89.16 °
Unit-cell angle γ angle_gamma	77.08 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1901
R_work r_work	0.1884
R_free r_free	0.2215

Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 1.7 A resolution (Triclinic form with one complete subunit built in alternate conformation)

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

Threonine dehydratase catabolic

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

2gn0__assembly_1__model_1

2gn0__assembly_1__model_1 | I(q)

2gn0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (2)

Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 1.7 A resolution (Triclinic form with one complete subunit built in alternate conformation)

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

Threonine dehydratase catabolic

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

2gn0__assembly_1__model_1

2gn0__assembly_1__model_1 | I(q)

2gn0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (2)