SAXSdb — 4grs

▼

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

Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 4	TYROSINE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8U0A9_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 104–333； UniProt 33–262 Author chain B； PDBConstruct 104–333； UniProt 33–262 Author chain C； PDBConstruct 104–333； UniProt 33–262 Author chain D； PDBConstruct 104–333； UniProt 33–262

Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase

Pyrococcus furiosus

UniProt Q9WYH8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 4	TYROSINE × 4 water × 4	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 1–103； UniProt 1–103 Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain C； PDBConstruct 1–103； UniProt 1–103 Author chain D； PDBConstruct 1–103； UniProt 1–103

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4grs
Deposition date deposition_date	2012-08-26
Structure title title	Crystal structure of a chimeric DAH7PS
Keywords keywords	;DAHP, DAHPS, DAH7PS, TIM BARREL, ACT DOMAIN, TRANSFERASE, ALLOSTERIC REGULATION, AROMATIC BIOSYNTHESIS, SHIKIMATE PATHWAY, TRANSFERABLE ALLOSTERY ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4grs__assembly_1__model_1

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

Download this curve (.dat)

4grs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4grs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.82 Å
Rg (electron density)	30.63 Å
Total Rg	31.35 Å
Atom count	10071
Residues	1329
Excluded volume	180310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4grs__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase
Molecular weight formula_weight	37114.7 kDa
EC 编号 ec_number	2.5.1.54
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	10092

MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVESVVRVLKPYKLVSREFHPEDTVIDLGDVKIGNGYFTIIAGPCSIESRDQIMKVAEFLAEVGIKVLRGGAFKPRTSPYSFQGYGEKALRWMREAADEYGLVTVTEVMDTRHVELVAKYSDILQIGARNSQNFELLKEVGKVENPVLLKRGMGNTIQELLYSAEYIMAQGNENVILCERGIRTFETATRFTLDISAVPVVKELSHLPIIVDPSHPAGRRSLVIPLAKAAYAIGADGIMVEVHPEPEKALSDSQQQLTFDDFLQLLKELEALGWKG

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	TYROSINE
Molecular weight formula_weight	181.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

▼

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4grsA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1140 — Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1

Domain ID domain_id	4grsA02
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	4grsB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1140 — Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1

Domain ID domain_id	4grsB02
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	4grsC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1140 — Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1

Domain ID domain_id	4grsC02
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	4grsD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1140 — Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1

Domain ID domain_id	4grsD02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

▶

Unit-cell length a length_a	76.901 Å
Unit-cell length b length_b	130.852 Å
Unit-cell length c length_c	138.070 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	3.000 Å
Low-resolution limit resolution_low	37.940 Å
R factor r_factor	0.1948
R_work r_work	0.1920
R_free r_free	0.2481

Crystal structure of a chimeric DAH7PS

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

Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate aldolase

State in the Current Structure

Other States of the Same Protein in the Database

Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate 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

4grs__assembly_1__model_1

4grs__assembly_1__model_1 | I(q)

4grs__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) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of a chimeric DAH7PS

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

Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate 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

Phospho-2-dehydro-3-deoxyheptonate aldolase, 2-dehydro-3-deoxyphosphoheptonate 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

4grs__assembly_1__model_1

4grs__assembly_1__model_1 | I(q)

4grs__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) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)