2yya

Crystal structure of GAR synthetase from Aquifex aeolicus

Method: X-RAY DIFFRACTION

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

Phosphoribosylamine--glycine ligase

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PUR2_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–424； UniProt 1–424 Author chain B； PDBConstruct 1–424； UniProt 1–424

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	2yya
Deposition date deposition_date	2007-04-27
Structure title title	Crystal structure of GAR synthetase from Aquifex aeolicus
Keywords keywords	;Glycinamide ribonucleotide synthetase, GAR synthetase, ATP binding, Purine nucleotide biosynthetic pathway, LIGASE, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; LIGASE
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.

2yya__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2yya__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yya__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.16 Å
Rg (electron density)	20.89 Å
Total Rg	21.84 Å
Atom count	3228
Residues	423
Excluded volume	57709 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yya__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yya__assembly_2__model_1`	monomeric （1）	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)

Entity 1 Entity 1 polymer

Description description	Phosphoribosylamine--glycine ligase
Molecular weight formula_weight	47500.5 kDa
EC 编号 ec_number	6.3.4.13
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	6553

MKVLVVGNGGREHAIAWKVAQSPLVKELYVAKGNAGIWEIAKRVDISPTDVEKLAEFAKNEGVDFTIVGPEAPLVEGIVDEFEKRGLKIFGPNKEAAKLEGSKAFAKTFMKKYGIPTARYEVFTDFEKAKEYVEKVGAPIVVKADGLAAGKGAVVCETVEKAIETLDRFLNKKIFGKSSERVVIEEFLEGEEASYIVMINGDRYVPLPTSQDHKRLLDEDKGPNTGGMGAYSPTPVINEEVEKRIREEIVERVIKGLKEEGIYYRGFLYAGLMITKEGPKVLEFNVRLGDPEAQPILMRVKNDFLETLLNFYEGKDVHIKEDERYALDVVLASRGYPEKPETGKIIHGLDYLKSMEDVVVFHAGTKKEGNFTVTSGGRVLNVCAYGKTLKEAKERAYEAIRYVCFEGMHYRKDIGDKAFKYLSE

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2yyaa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.30 — PreATP-grasp domain
Superfamily Superfamily superfamily	c.30.1 — PreATP-grasp domain
Family Family family	c.30.1.0 — automated matches

Domain ID domain_id	d2yyaa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.0 — automated matches

Domain ID domain_id	d2yyaa3
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
Family Family family	b.84.2.0 — automated matches

Domain ID domain_id	d2yyab1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.30 — PreATP-grasp domain
Superfamily Superfamily superfamily	c.30.1 — PreATP-grasp domain
Family Family family	c.30.1.0 — automated matches

Domain ID domain_id	d2yyab2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.0 — automated matches

Domain ID domain_id	d2yyab3
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
Family Family family	b.84.2.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2yyaA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2yyaA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

Domain ID domain_id	2yyaA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

Domain ID domain_id	2yyaA04
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	600 — Glycinamide Ribonucleotide Synthetase; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Phosphoribosylglycinamide synthetase, C-terminal domain

Domain ID domain_id	2yyaB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2yyaB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

Domain ID domain_id	2yyaB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

Domain ID domain_id	2yyaB04
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	600 — Glycinamide Ribonucleotide Synthetase; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Phosphoribosylglycinamide synthetase, C-terminal domain

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Unit-cell length a length_a	97.262 Å
Unit-cell length b length_b	45.152 Å
Unit-cell length c length_c	103.484 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	49.550 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2490

Crystal structure of GAR synthetase from Aquifex aeolicus

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

Phosphoribosylamine--glycine ligase

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

2yya__assembly_2__model_1

2yya__assembly_2__model_1 | I(q)

2yya__assembly_2__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) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of GAR synthetase from Aquifex aeolicus

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

Phosphoribosylamine--glycine ligase

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

2yya__assembly_2__model_1

2yya__assembly_2__model_1 | I(q)

2yya__assembly_2__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) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)