SAXSdb — 2ywx

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

Phosphoribosylaminoimidazole carboxylase catalytic subunit

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PUR6_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–157； UniProt 1–157

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	2ywx
Deposition date deposition_date	2007-04-23
Structure title title	Crystal structure of phosphoribosylaminoimidazole carboxylase catalytic subunit from Methanocaldococcus jannaschii
Keywords keywords	;Rossmann fold, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

2ywx__assembly_1__model_1

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

Download this curve (.dat)

2ywx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ywx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.55 Å
Rg (electron density)	31.49 Å
Total Rg	32.34 Å
Atom count	9504
Residues	1256
Excluded volume	174090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ywx__assembly_1__model_1`	octameric （8）	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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2ywxa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.8 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
Family Family family	c.23.8.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	2ywxA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

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Unit-cell length a length_a	100.887 Å
Unit-cell length b length_b	100.887 Å
Unit-cell length c length_c	70.912 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 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	31.900 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2400

Description description	Phosphoribosylaminoimidazole carboxylase catalytic subunit
Molecular weight formula_weight	16974.0 kDa
EC 编号 ec_number	4.1.1.21
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1213

Crystal structure of phosphoribosylaminoimidazole carboxylase catalytic subunit from Methanocaldococcus jannaschii

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

Phosphoribosylaminoimidazole carboxylase catalytic subunit

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

2ywx__assembly_1__model_1

2ywx__assembly_1__model_1 | I(q)

2ywx__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
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	25

Crystal structure of phosphoribosylaminoimidazole carboxylase catalytic subunit from Methanocaldococcus jannaschii

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

Phosphoribosylaminoimidazole carboxylase catalytic subunit

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

2ywx__assembly_1__model_1

2ywx__assembly_1__model_1 | I(q)

2ywx__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)