SAXSdb — 3gc2

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

o-succinylbenzoate synthase

Salmonella typhimurium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SUCCINIC ACID × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SODIUM ION × 2 CHLORIDE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MENC_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–323； UniProt 1–320

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	3gc2
Deposition date deposition_date	2009-02-21
Structure title title	1.85 Angstrom Crystal Structure of O-succinylbenzoate Synthase from Salmonella typhimurium in Complex with Succinic Acid
Keywords keywords	;O-succinylbenzoate synthase, Succinic Acid, idp00994, Lyase, Magnesium, Menaquinone biosynthesis, Metal-binding, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID ;; 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.

3gc2__assembly_1__model_1

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

Download this curve (.dat)

3gc2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gc2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.28 Å
Rg (electron density)	20.19 Å
Total Rg	21.13 Å
Atom count	2536
Residues	316
Excluded volume	45304 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gc2__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	o-succinylbenzoate synthase
Molecular weight formula_weight	35952.0 kDa
EC 编号 ec_number	4.2.1.113
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3044

SNAMRSAQVYRWQIPMDAGVVLRDRRLKTRDGLYVCLRDGEREGWGEISPLPGFSQETWEEAQTALLTWVNDWLQGSEGLPEMPSVAFGASCALAELTGVLPEAADYRAAPLCTGDPDDLVLRLADMPGEKIAKVKVGLYEAVRDGMVVNLLLEAIPDLHLRLDANRAWTPLKAQQFAKYVNPDYRARIAFLEEPCKTRDDSRAFARETGIAIAWDESLREADFTFEAEEGVRAVVIKPTLTGSLDKVREQVAAAHALGLTAVISSSIESSLGLTQLARIAAWLTPGTLPGLDTLHLMQAQQIRPWPGSALPCLKREELERLL

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	SUCCINIC ACID
Molecular weight formula_weight	118.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	316

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3gc2a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
Family Family family	d.54.1.0 — automated matches

Domain ID domain_id	d3gc2a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
Family Family family	c.1.11.2 — D-glucarate dehydratase-like

Domain ID domain_id	d3gc2a3
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	3gc2A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	3gc2A02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

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Unit-cell length a length_a	149.968 Å
Unit-cell length b length_b	149.968 Å
Unit-cell length c length_c	39.120 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	27.070 Å
R factor r_factor	0.1564
R_work r_work	0.1550
R_free r_free	0.1848

1.85 Angstrom Crystal Structure of O-succinylbenzoate Synthase from Salmonella typhimurium in Complex with Succinic Acid

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

o-succinylbenzoate synthase

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

3gc2__assembly_1__model_1

3gc2__assembly_1__model_1 | I(q)

3gc2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

1.85 Angstrom Crystal Structure of O-succinylbenzoate Synthase from Salmonella typhimurium in Complex with Succinic Acid

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

o-succinylbenzoate synthase

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

3gc2__assembly_1__model_1

3gc2__assembly_1__model_1 | I(q)

3gc2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)