2a7w

Crystal Structure of Phosphoribosyl-ATP Pyrophosphatase from Chromobacterium violaceum (ATCC 12472). NESG TARGET CVR7

Method: X-RAY DIFFRACTION

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

Phosphoribosyl-ATP pyrophosphatase

Chromobacterium violaceum

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
2	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count
3	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_CHRVO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–108； UniProt 1–108 Author chain B； PDBConstruct 1–108； UniProt 1–108 Author chain C； PDBConstruct 1–108； UniProt 1–108 Author chain D； PDBConstruct 1–108； UniProt 1–108 Author chain E； PDBConstruct 1–108； UniProt 1–108 Author chain F； PDBConstruct 1–108； UniProt 1–108 Author chain G； PDBConstruct 1–108； UniProt 1–108 Author chain H； PDBConstruct 1–108； UniProt 1–108 Author chain I； PDBConstruct 1–108； UniProt 1–108 Author chain J； PDBConstruct 1–108； UniProt 1–108 Author chain K； PDBConstruct 1–108； UniProt 1–108 Author chain L； PDBConstruct 1–108； UniProt 1–108

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	2a7w
Deposition date deposition_date	2005-07-06
Structure title title	Crystal Structure of Phosphoribosyl-ATP Pyrophosphatase from Chromobacterium violaceum (ATCC 12472). NESG TARGET CVR7
Keywords keywords	;PHOSPHORIBOSYL-ATP 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.

2a7w__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2a7w__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2a7w__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	22.25 Å
Rg (electron density)	21.06 Å
Total Rg	21.87 Å
Atom count	2908
Residues	352
Excluded volume	51935 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2a7w__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2a7w__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2a7w__assembly_3__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) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2a7wa1
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	d2a7wb_
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	d2a7wc_
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	d2a7wd_
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	d2a7we_
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	d2a7wf_
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	d2a7wg_
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	d2a7wh_
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	d2a7wi_
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	d2a7wj_
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	d2a7wk_
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	d2a7wl_
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 (12 domains)

Domain ID domain_id	2a7wA00
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	2a7wB00
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	2a7wC00
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	2a7wD00
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	2a7wE00
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	2a7wF00
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	2a7wG00
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	2a7wH00
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	2a7wI00
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	2a7wJ00
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	2a7wK00
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	2a7wL00
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	97.938 Å
Unit-cell length b length_b	67.544 Å
Unit-cell length c length_c	113.512 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	29.310 Å
R factor r_factor	0.2582
R_work r_work	0.2582
R_free r_free	0.2799

Description description	Phosphoribosyl-ATP pyrophosphatase
Molecular weight formula_weight	13418.7 kDa
EC 编号 ec_number	3.6.1.31
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	9063

Crystal Structure of Phosphoribosyl-ATP Pyrophosphatase from Chromobacterium violaceum (ATCC 12472). NESG TARGET CVR7

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

2a7w__assembly_3__model_1

2a7w__assembly_3__model_1 | I(q)

2a7w__assembly_3__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Chromobacterium violaceum
NCBI taxonomy ID ncbi_taxonomy_id	536
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	339

Crystal Structure of Phosphoribosyl-ATP Pyrophosphatase from Chromobacterium violaceum (ATCC 12472). NESG TARGET CVR7

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

2a7w__assembly_3__model_1

2a7w__assembly_3__model_1 | I(q)

2a7w__assembly_3__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)