3fq3

Crystal structure of inorganic phosphatase from brucella melitensis

Method: X-RAY DIFFRACTION

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

Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase

Brucella melitensis biovar Abortus 2308

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	PHOSPHATE ION × 12 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	PHOSPHATE ION × 9 water × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	PHOSPHATE ION × 6 water × 3	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	PHOSPHATE ION × 6 water × 3	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 3	PHOSPHATE ION × 5 water × 3	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 3	PHOSPHATE ION × 4 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2YR76_BRUA2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–197； UniProt 1–176 Author chain B； PDBConstruct 22–197； UniProt 1–176 Author chain C； PDBConstruct 22–197； UniProt 1–176 Author chain D； PDBConstruct 22–197； UniProt 1–176 Author chain E； PDBConstruct 22–197； UniProt 1–176 Author chain F； PDBConstruct 22–197； UniProt 1–176 Author chain G； PDBConstruct 22–197； UniProt 1–176 Author chain H； PDBConstruct 22–197； UniProt 1–176 Author chain I； PDBConstruct 22–197； UniProt 1–176 Author chain J； PDBConstruct 22–197； UniProt 1–176 Author chain K； PDBConstruct 22–197； UniProt 1–176 Author chain L； PDBConstruct 22–197； UniProt 1–176

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	3fq3
Deposition date deposition_date	2009-01-06
Structure title title	Crystal structure of inorganic phosphatase from brucella melitensis
Keywords keywords	;SSGCID, INORGANIC PHOSPHATASE, BRUCELLA MELITENSIS, Hydrolase, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease ;; 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.

3fq3__assembly_3__model_1

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

Download this curve (.dat)

3fq3__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fq3__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.69 Å
Rg (electron density)	24.42 Å
Total Rg	25.18 Å
Atom count	4121
Residues	521
Excluded volume	73317 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fq3__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fq3__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3fq3__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3fq3__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3fq3__assembly_5__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3fq3__assembly_6__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
Molecular weight formula_weight	22136.3 kDa
EC 编号 ec_number	3.6.1.1
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

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	18458

MAHHHHHHMGTLEAQTQGPGSMNIDAISIGSNPPEDVNVIIEVPVGGQPIKYEMDKKAGALIVDRFLYTPMTYPGNYGFVPHTLSEDGDPIDVLVCNTRPLIPGCVINVRPIGVLVMEDNSGKDEKIIAVPSPHLTRRYEKIHDYTDMPEITLKQIAHFFEHYKDLEPGKWVKIGDWGDEDYARKFIVEAIERAKGK

Source Source

Source organism organism	Brucella melitensis biovar Abortus 2308
NCBI taxonomy ID ncbi_taxonomy_id	359391
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2053

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3fq3a_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3b_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3c_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3d_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3e_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3f_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3g_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3h_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3i_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3j_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3k_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

Domain ID domain_id	d3fq3l_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.5 — Inorganic pyrophosphatase
Family Family family	b.40.5.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	3fq3A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3C00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3D00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3E00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3F00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3G00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3H00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3I00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3J00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3K00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

Domain ID domain_id	3fq3L00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	80 — Inorganic Pyrophosphatase
Homologous superfamily homologous superfamily	10 — Inorganic pyrophosphatase

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Unit-cell length a length_a	157.830 Å
Unit-cell length b length_b	157.830 Å
Unit-cell length c length_c	106.310 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	48

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.870 Å
R factor r_factor	0.1690
R_work r_work	0.1670
R_free r_free	0.2090

Crystal structure of inorganic phosphatase from brucella melitensis

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

Inorganic pyrophosphatase:Bacterial/Archaeal inorganic 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

3fq3__assembly_3__model_1

3fq3__assembly_3__model_1 | I(q)

3fq3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of inorganic phosphatase from brucella melitensis

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

Inorganic pyrophosphatase:Bacterial/Archaeal inorganic 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

3fq3__assembly_3__model_1

3fq3__assembly_3__model_1 | I(q)

3fq3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)