SAXSdb — 3ird

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

Dihydrodipicolinate synthase

Clostridium botulinum A str. Hall

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	D-MALATE × 4 SODIUM ION × 4 CHLORIDE ION × 8 GLYCEROL × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5I6N2_CLOBH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–291； UniProt 2–292

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	3ird
Deposition date deposition_date	2009-08-22
Structure title title	Structure of dihydrodipicolinate synthase from Clostridium botulinum
Keywords keywords	;Clostridium botulinum, dihydrodipicolinate synthase, Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lyase, Lysine biosynthesis, Schiff base ;; 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.

3ird__assembly_1__model_1

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

Download this curve (.dat)

3ird__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ird__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.84 Å
Rg (electron density)	30.80 Å
Total Rg	31.58 Å
Atom count	8892
Residues	1164
Excluded volume	161410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ird__assembly_1__model_1`	tetrameric （4）	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	Dihydrodipicolinate synthase
Molecular weight formula_weight	31551.6 kDa
EC 编号 ec_number	4.2.1.52
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	2495

SIFKGSGVAIITPFTNTGVDFDKLSELIEWHIKSKTDAIIVCGTTGEATTMTETERKETIKFVIDKVNKRIPVIAGTGSNNTAASIAMSKWAESIGVDGLLVITPYYNKTTQKGLVKHFKAVSDAVSTPIIIYNVPGRTGLNITPGTLKELCEDKNIVAVKEASGNISQIAQIKALCGDKLDIYSGNDDQIIPILALGGIGVISVLANVIPEDVHNMCELYLNGKVNEALKIQLDSLALTNALFIETNPIPVKTAMNLMNMKVGDLRLPLCEMNENNLEILKKELKAYNLM

Source Source

Source organism organism	Clostridium botulinum A str. Hall
NCBI taxonomy ID ncbi_taxonomy_id	441771
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	D-MALATE
Molecular weight formula_weight	134.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	262

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3irda_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

CATH v4.4 (1 domains)

Domain ID domain_id	3irdA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	92.810 Å
Unit-cell length b length_b	92.810 Å
Unit-cell length c length_c	60.350 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 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.230 Å
Low-resolution limit resolution_low	34.200 Å
R factor r_factor	0.1423
R_work r_work	0.1349
R_free r_free	0.2093

Structure of dihydrodipicolinate synthase from Clostridium botulinum

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

Dihydrodipicolinate 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

3ird__assembly_1__model_1

3ird__assembly_1__model_1 | I(q)

3ird__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of dihydrodipicolinate synthase from Clostridium botulinum

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

Dihydrodipicolinate 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

3ird__assembly_1__model_1

3ird__assembly_1__model_1 | I(q)

3ird__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)