SAXSdb — 1w3n

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

2-KETO-3-DEOXY GLUCONATE ALDOLASE

SULFOLOBUS SOLFATARICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	3-DEOXY-D-ARABINO-HEXONIC ACID × 4 GLYCEROL × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O54288
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–294； UniProt 1–294 Author chain B； PDBConstruct 1–294； UniProt 1–294 Author chain C； PDBConstruct 1–294； UniProt 1–294 Author chain D； PDBConstruct 1–294； UniProt 1–294

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	1w3n
Deposition date deposition_date	2004-07-17
Structure title title	Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDG
Keywords keywords	ALDOLASE, ARCHAEAL METABOLISM, D-KDG; ALDOLASE
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.

1w3n__assembly_1__model_1

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

Download this curve (.dat)

1w3n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1w3n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.28 Å
Rg (electron density)	31.23 Å
Total Rg	32.11 Å
Atom count	9364
Residues	1172
Excluded volume	169670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1w3n__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 (4)

Entity 1 Entity 1 polymer

Description description	2-KETO-3-DEOXY GLUCONATE ALDOLASE
Molecular weight formula_weight	33152.4 kDa
EC 编号 ec_number	4.1.2.20
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	10314

MPEIITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNKIIFQVGGLNLDDAIRLAKLSKDFDIVGIASYAPYYYPRMSEKHLVKYFKTLCEVSPHPVYLYNYPTATGKDIDAKVAKEIGCFTGVKDTIENIIHTLDYKRLNPNMLVYSGSDMLIATVASTGLDGNVAAGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGYDLGYPRPPIFPLDDEEERQLIKKVEGIRAKLVELKILKE

Source Source

Source organism organism	SULFOLOBUS SOLFATARICUS
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	3-DEOXY-D-ARABINO-HEXONIC ACID
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	812

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1w3na_
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

Domain ID domain_id	d1w3nb_
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

Domain ID domain_id	d1w3nc_
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

Domain ID domain_id	d1w3nd_
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 (4 domains)

Domain ID domain_id	1w3nA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1w3nB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1w3nC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1w3nD00
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	83.797 Å
Unit-cell length b length_b	131.269 Å
Unit-cell length c length_c	132.759 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1570
R_work r_work	0.1510
R_free r_free	0.2130

Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDG

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

2-KETO-3-DEOXY GLUCONATE 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

1w3n__assembly_1__model_1

1w3n__assembly_1__model_1 | I(q)

1w3n__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDG

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

2-KETO-3-DEOXY GLUCONATE 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

1w3n__assembly_1__model_1

1w3n__assembly_1__model_1 | I(q)

1w3n__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)