SAXSdb — 3pg8

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

Phospho-2-dehydro-3-deoxyheptonate aldolase

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 6 AZIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AROF_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–272； UniProt 71–338 Author chain B； PDBConstruct 5–272； UniProt 71–338

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	3pg8
Deposition date deposition_date	2010-10-31
Structure title title	Truncated form of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Thermotoga maritima
Keywords keywords	Thermotoga maritima, DAH7PS, Shikimate pathway, aromatic biosynthesis, transferase, Tim barrel; 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.

3pg8__assembly_1__model_1

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

Download this curve (.dat)

3pg8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pg8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.42 Å
Rg (electron density)	24.45 Å
Total Rg	25.28 Å
Atom count	3978
Residues	524
Excluded volume	71441 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pg8__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Phospho-2-dehydro-3-deoxyheptonate aldolase
Molecular weight formula_weight	29950.3 kDa
EC 编号 ec_number	2.5.1.54
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4291

GSFTLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVKVN

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	238

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3pg8a1
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	d3pg8a2
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	d3pg8b1
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	d3pg8b2
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	3pg8A00
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	3pg8B00
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	53.510 Å
Unit-cell length b length_b	55.456 Å
Unit-cell length c length_c	166.935 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	38.570 Å
R factor r_factor	0.1580
R_work r_work	0.1546
R_free r_free	0.2094

Truncated form of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Thermotoga maritima

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

Phospho-2-dehydro-3-deoxyheptonate 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

3pg8__assembly_1__model_1

3pg8__assembly_1__model_1 | I(q)

3pg8__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Truncated form of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Thermotoga maritima

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

Phospho-2-dehydro-3-deoxyheptonate 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

3pg8__assembly_1__model_1

3pg8__assembly_1__model_1 | I(q)

3pg8__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)