SAXSdb — 4c1l

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

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	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (II) ION × 4 CHLORIDE ION × 8 POTASSIUM ION × 4 PENTAETHYLENE GLYCOL × 2 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 1–262； UniProt 1–262 Author chain B； PDBConstruct 1–262； UniProt 1–262

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	4c1l
Deposition date deposition_date	2013-08-13
Structure title title	Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase I181D interface mutant
Keywords keywords	TRANSFERASE, SHIKIMATE PATHWAY, INTERFACE MUTANT; 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.

4c1l__assembly_1__model_1

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

Download this curve (.dat)

4c1l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4c1l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.70 Å
Rg (electron density)	29.79 Å
Total Rg	30.40 Å
Atom count	8260
Residues	1048
Excluded volume	148780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4c1l__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	2-dehydro-3-deoxyphosphoheptonate aldolase
Molecular weight formula_weight	29262.6 kDa
EC 编号 ec_number	2.5.1.54
Mutation mutation	I181D
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	4707

MKYSKEYKEKTVVKINDVKFGEGFTIIAGPCSIESRDQIMKVAEFLAEVGIKVLRGGAFKPRTSPYSFQGYGEKALRWMREAADEYGLVTVTEVMDTRHVELVAKYSDILQIGARNSQNFELLKEVGKVENPVLLKRGMGNTIQELLYSAEYIMAQGNENVILCERGIRTFETATRFTLDDSAVPVVKELSHLPIIVDPSHPAGRRSLVIPLAKAAYAIGADGIMVEVHPEPEKALSDSQQQLTFDDFLQLLKELEALGWKG

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	422

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4c1lA00
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	4c1lB00
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	87.942 Å
Unit-cell length b length_b	110.923 Å
Unit-cell length c length_c	143.531 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	43.970 Å
R factor r_factor	0.1652
R_work r_work	0.1642
R_free r_free	0.1833

Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase I181D interface mutant

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

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

4c1l__assembly_1__model_1

4c1l__assembly_1__model_1 | I(q)

4c1l__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

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase I181D interface mutant

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

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

4c1l__assembly_1__model_1

4c1l__assembly_1__model_1 | I(q)

4c1l__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

CATH v4.4 (2 domains)

7. Citations (1)