SAXSdb — 1yvw

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

Phosphoribosyl-ATP pyrophosphatase

Bacillus cereus

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	HIS2_BACCR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–107； UniProt 1–107 Author chain B； PDBConstruct 1–107； UniProt 1–107 Author chain C； PDBConstruct 1–107； UniProt 1–107 Author chain D； PDBConstruct 1–107； UniProt 1–107

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	1yvw
Deposition date deposition_date	2005-02-16
Structure title title	Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from Bacillus cereus. NESGC target BcR13.
Keywords keywords	;HELIX BUNDLE, HISTIDINE BIOSYNTHESIS, pyrophosphatase, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, HYDROLASE ;; HYDROLASE
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.

1yvw__assembly_1__model_1

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

Download this curve (.dat)

1yvw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yvw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.13 Å
Rg (electron density)	21.12 Å
Total Rg	21.91 Å
Atom count	2988
Residues	360
Excluded volume	54239 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yvw__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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1yvwa1
Class class	a — All alpha proteins
Fold Fold fold	a.204 — all-alpha NTP pyrophosphatases
Superfamily Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
Family Family family	a.204.1.4 — HisE-like (PRA-PH)

Domain ID domain_id	d1yvwb_
Class class	a — All alpha proteins
Fold Fold fold	a.204 — all-alpha NTP pyrophosphatases
Superfamily Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
Family Family family	a.204.1.4 — HisE-like (PRA-PH)

Domain ID domain_id	d1yvwc_
Class class	a — All alpha proteins
Fold Fold fold	a.204 — all-alpha NTP pyrophosphatases
Superfamily Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
Family Family family	a.204.1.4 — HisE-like (PRA-PH)

Domain ID domain_id	d1yvwd_
Class class	a — All alpha proteins
Fold Fold fold	a.204 — all-alpha NTP pyrophosphatases
Superfamily Superfamily superfamily	a.204.1 — all-alpha NTP pyrophosphatases
Family Family family	a.204.1.4 — HisE-like (PRA-PH)

CATH v4.4 (4 domains)

Domain ID domain_id	1yvwA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1080 — MazG-like

Domain ID domain_id	1yvwB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1080 — MazG-like

Domain ID domain_id	1yvwC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1080 — MazG-like

Domain ID domain_id	1yvwD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1080 — MazG-like

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Unit-cell length a length_a	81.959 Å
Unit-cell length b length_b	81.959 Å
Unit-cell length c length_c	222.978 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	29.060 Å
R factor r_factor	0.2440
R_work r_work	0.2440
R_free r_free	0.2630

Description description	Phosphoribosyl-ATP pyrophosphatase
Molecular weight formula_weight	13678.2 kDa
EC 编号 ec_number	3.6.1.31
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	3157

Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from Bacillus cereus. NESGC target BcR13.

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

Phosphoribosyl-ATP pyrophosphatase

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

1yvw__assembly_1__model_1

1yvw__assembly_1__model_1 | I(q)

1yvw__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Bacillus cereus
NCBI taxonomy ID ncbi_taxonomy_id	1396
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	169

Crystal structure of Phosphoribosyl-ATP pyrophosphohydrolase from Bacillus cereus. NESGC target BcR13.

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

Phosphoribosyl-ATP pyrophosphatase

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

1yvw__assembly_1__model_1

1yvw__assembly_1__model_1 | I(q)

1yvw__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)