SAXSdb — 3e9a

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

2-dehydro-3-deoxyphosphooctonate aldolase

Vibrio cholerae O1 biovar El tor

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDSA_VIBCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–286； UniProt 1–283

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	3e9a
Deposition date deposition_date	2008-08-21
Structure title title	Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Vibrio cholerae O1 biovar eltor str. N16961
Keywords keywords	;2-dehydro-3-deoxyphosphooctonate aldolase, 3-deoxy-8-phosphooctulonate synthase, Lipopolysaccharide biosynthesis, CSGID, Transferase, Structural Genomics, Center for Structural Genomics of Infectious Diseases ;; 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.

3e9a__assembly_1__model_1

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

Download this curve (.dat)

3e9a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e9a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.41 Å
Rg (electron density)	30.62 Å
Total Rg	31.33 Å
Atom count	8452
Residues	1100
Excluded volume	151210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e9a__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3e9a__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3e9a__assembly_3__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	2-dehydro-3-deoxyphosphooctonate aldolase
Molecular weight formula_weight	31084.7 kDa
EC 编号 ec_number	2.5.1.55
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	2296

SNAMEHKIVHVGDIPVANDKPFTLFAGMNVLESRDLAMQICEHYVKVTDKLGIPYVFKASFDKANRSSVHSYRGPGLEEGMKIFQELKETFGVKIITDVHTEAQAQPVADVVDVIQLPAFLARQTDLVEAMAKTGAVINVKKPQFMSPGQVGNIVEKFAECGNDKVILCERGSCHGYDNLVVDMLGFGVMKQASNGSPIIFDVTHSLQMRDPSGAASGGRREQTVELAKAGLATGIAGLFIEAHPNPDKARCDGPSALPLDKLEPFLAQMKALDDLIKSFAHIDIR

Source Source

Source organism organism	Vibrio cholerae O1 biovar El tor
NCBI taxonomy ID ncbi_taxonomy_id	686
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3e9aa1
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.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d3e9aa2
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 (1 domains)

Domain ID domain_id	3e9aA00
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	117.187 Å
Unit-cell length b length_b	117.187 Å
Unit-cell length c length_c	117.187 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	24

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1780
R_work r_work	0.1760
R_free r_free	0.2150

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Vibrio cholerae O1 biovar eltor str. N16961

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

2-dehydro-3-deoxyphosphooctonate aldolase

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

3e9a__assembly_1__model_1

3e9a__assembly_1__model_1 | I(q)

3e9a__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Vibrio cholerae O1 biovar eltor str. N16961

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

2-dehydro-3-deoxyphosphooctonate aldolase

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

3e9a__assembly_1__model_1

3e9a__assembly_1__model_1 | I(q)

3e9a__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)