2qfp

Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride

Method: X-RAY DIFFRACTION

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

Purple acid phosphatase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 ZINC ION × 2 SULFATE ION × 4 FLUORIDE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 SODIUM ION × 6 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 2 ZINC ION × 2 SULFATE ION × 4 FLUORIDE ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 SODIUM ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O24319_PHAVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–424； UniProt 36–459 Author chain B； PDBConstruct 1–424； UniProt 36–459 Author chain C； PDBConstruct 1–424； UniProt 36–459 Author chain D； PDBConstruct 1–424； UniProt 36–459

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	2qfp
Deposition date deposition_date	2007-06-27
Structure title title	Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride
Keywords keywords	binuclear, Fe-Zn, 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.

2qfp__assembly_1__model_1

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

Download this curve (.dat)

2qfp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qfp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.22 Å
Rg (electron density)	29.36 Å
Total Rg	30.09 Å
Atom count	7118
Residues	848
Excluded volume	125500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qfp__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qfp__assembly_2__model_1`	dimeric （2）	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 (8)

Entity 1 Entity 1 polymer

Description description	Purple acid phosphatase
Molecular weight formula_weight	49312.1 kDa
EC 编号 ec_number	3.1.3.2
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14782

RDMPLDSDVFRVPPGYNAPQQVHITQGDLVGRAMIISWVTMDEPGSSAVRYWSEKNGRKRIAKGKMSTYRFFNYSSGFIHHTTIRKLKYNTKYYYEVGLRNTTRRFSFITPPQTGLDVPYTFGLIGDLGQSFDSNTTLSHYELSPKKGQTVLFVGDLSYADRYPNHDNVRWDTWGRFTERSVAYQPWIWTAGNHEIEFAPEINETEPFKPFSYRYHVPYEASQSTSPFWYSIKRASAHIIVLSSYSAYGRGTPQYTWLKKELRKVKRSETPWLIVLMHSPLYNSYNHHFMEGEAMRTKFEAWFVKYKVDVVFAGHVHAYERSERVSNIAYKITNGLCTPVKDQSAPVYITIGDAGNYGVIDSNMIQPQPEYSAFREASFGHGMFDIKNRTHAHFSWNRNQDGVAVEADSVWFFNRHWYPVDDST

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	FLUORIDE ION
Molecular weight formula_weight	19.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	16

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	547

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2qfpa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.12 — Purple acid phosphatase, N-terminal domain
Family Family family	b.1.12.0 — automated matches

Domain ID domain_id	d2qfpa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.1 — Purple acid phosphatase-like

Domain ID domain_id	d2qfpb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.12 — Purple acid phosphatase, N-terminal domain
Family Family family	b.1.12.0 — automated matches

Domain ID domain_id	d2qfpb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.1 — Purple acid phosphatase-like

Domain ID domain_id	d2qfpc1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.12 — Purple acid phosphatase, N-terminal domain
Family Family family	b.1.12.0 — automated matches

Domain ID domain_id	d2qfpc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.1 — Purple acid phosphatase-like

Domain ID domain_id	d2qfpd1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.12 — Purple acid phosphatase, N-terminal domain
Family Family family	b.1.12.0 — automated matches

Domain ID domain_id	d2qfpd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.1 — Purple acid phosphatase-like

CATH v4.4 (8 domains)

Domain ID domain_id	2qfpA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	380 — Purple acid phosphatase-like, N-terminal

Domain ID domain_id	2qfpA02
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	2qfpB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	380 — Purple acid phosphatase-like, N-terminal

Domain ID domain_id	2qfpB02
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	2qfpC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	380 — Purple acid phosphatase-like, N-terminal

Domain ID domain_id	2qfpC02
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	2qfpD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	380 — Purple acid phosphatase-like, N-terminal

Domain ID domain_id	2qfpD02
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

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Unit-cell length a length_a	85.719 Å
Unit-cell length b length_b	188.466 Å
Unit-cell length c length_c	192.398 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	33.000 Å
R factor r_factor	0.2260
R_work r_work	0.2240
R_free r_free	0.2540

Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride

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

Purple acid phosphatase

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

2qfp__assembly_1__model_1

2qfp__assembly_1__model_1 | I(q)

2qfp__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride

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

Purple acid phosphatase

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

2qfp__assembly_1__model_1

2qfp__assembly_1__model_1 | I(q)

2qfp__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)