1dof

THE CRYSTAL STRUCTURE OF ADENYLOSUCCINATE LYASE FROM PYROBACULUM AEROPHILUM: INSIGHTS INTO THERMAL STABILITY AND HUMAN PATHOLOGY

Method: X-RAY DIFFRACTION

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

ADENYLOSUCCINATE LYASE

Pyrobaculum aerophilum

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8ZY28_PYRAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–403； UniProt 1–403 Author chain B； PDBConstruct 1–403； UniProt 1–403 Author chain C； PDBConstruct 1–403； UniProt 1–403 Author chain D； PDBConstruct 1–403； UniProt 1–403

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	1dof
Deposition date deposition_date	1999-12-20
Structure title title	THE CRYSTAL STRUCTURE OF ADENYLOSUCCINATE LYASE FROM PYROBACULUM AEROPHILUM: INSIGHTS INTO THERMAL STABILITY AND HUMAN PATHOLOGY
Keywords keywords	purine biosynthesis, lyase; LYASE
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.

1dof__assembly_1__model_1

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

Download this curve (.dat)

1dof__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dof__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.22 Å
Rg (electron density)	33.16 Å
Total Rg	33.86 Å
Atom count	11872
Residues	1540
Excluded volume	212280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dof__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 (2)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dofa_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.1 — L-aspartase/fumarase

Domain ID domain_id	d1dofb_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.1 — L-aspartase/fumarase

Domain ID domain_id	d1dofc_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.1 — L-aspartase/fumarase

Domain ID domain_id	d1dofd_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.1 — L-aspartase/fumarase

CATH v4.4 (12 domains)

Domain ID domain_id	1dofA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1dofA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1dofA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

Domain ID domain_id	1dofB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1dofB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1dofB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

Domain ID domain_id	1dofC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1dofC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1dofC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

Domain ID domain_id	1dofD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1dofD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1dofD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	40 — Ribonucleotide Reductase Protein R1; domain 1
Homologous superfamily homologous superfamily	30 — Fumarase/aspartase (C-terminal domain)

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Unit-cell length a length_a	65.620 Å
Unit-cell length b length_b	150.310 Å
Unit-cell length c length_c	173.010 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	50.000 Å
R factor r_factor	—
R_work r_work	0.2030
R_free r_free	0.2450

Description description	ADENYLOSUCCINATE LYASE
Molecular weight formula_weight	45423.2 kDa
EC 编号 ec_number	4.3.2.2
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12664

THE CRYSTAL STRUCTURE OF ADENYLOSUCCINATE LYASE FROM PYROBACULUM AEROPHILUM: INSIGHTS INTO THERMAL STABILITY AND HUMAN PATHOLOGY

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

ADENYLOSUCCINATE LYASE

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

1dof__assembly_1__model_1

1dof__assembly_1__model_1 | I(q)

1dof__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Pyrobaculum aerophilum
NCBI taxonomy ID ncbi_taxonomy_id	13773
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	792

THE CRYSTAL STRUCTURE OF ADENYLOSUCCINATE LYASE FROM PYROBACULUM AEROPHILUM: INSIGHTS INTO THERMAL STABILITY AND HUMAN PATHOLOGY

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

ADENYLOSUCCINATE LYASE

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

1dof__assembly_1__model_1

1dof__assembly_1__model_1 | I(q)

1dof__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)