SAXSdb — 2zoa

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

Phosphohydrolase

Enterobacter aerogenes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	FE (II) ION × 12 MALONATE ION × 6 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FE (II) ION × 4 MALONATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6XBH1_ENTAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–274； UniProt 1–274 Author chain B； PDBConstruct 1–274； UniProt 1–274

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	2zoa
Deposition date deposition_date	2008-05-07
Structure title title	Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) COLLECTED AT 1.280 ANGSTROM
Keywords keywords	MALONATE, METALLOENZYME, IRON, PHOSPHODIESTERASE, 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.

2zoa__assembly_1__model_1

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

Download this curve (.dat)

2zoa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zoa__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.43 Å
Rg (electron density)	34.65 Å
Total Rg	35.15 Å
Atom count	12852
Residues	1626
Excluded volume	226520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zoa__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zoa__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 (4)

Entity 1 Entity 1 polymer

Description description	Phosphohydrolase
Molecular weight formula_weight	30772.6 kDa
EC 编号 ec_number	3.1.4.46
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4438

MLLAHISDTHFRSRGEKLYGFIDVNAANADVVSQLNALRERPDAVVVSGDIVNCGRPEEYQVARQILGSLNYPLYLIPGNHDDKALFLEYLQPLCPQLGSDANNMRCAVDDFATRLLFIDSSRAGTSKGWLTDETISWLEAQLFEGGDKPATIFMHHPPLPLGNAQMDPIACENGHRLLALVERFPSLTRIFCGHNHSLTMTQYRQALISTLPGTVHQVPYCHADTDPYYDLSPASCLMHRQVGEQWVSYQHSLAHYAGPWLYDENISCPTEER

Source Source

Source organism organism	Enterobacter aerogenes
NCBI taxonomy ID ncbi_taxonomy_id	548
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (II) 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	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	154

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2zoaa_
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.159.1.11 — GpdQ-like

Domain ID domain_id	d2zoab_
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.159.1.11 — GpdQ-like

CATH v4.4 (4 domains)

Domain ID domain_id	2zoaA01
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	40 — GpdQ, catalytic alpha/beta sandwich domain

Domain ID domain_id	2zoaA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	180 — GpdQ, beta-strand dimerisation domain

Domain ID domain_id	2zoaB01
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	40 — GpdQ, catalytic alpha/beta sandwich domain

Domain ID domain_id	2zoaB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	750 — Transcription Regulator spoIIAA
Homologous superfamily homologous superfamily	180 — GpdQ, beta-strand dimerisation domain

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Unit-cell length a length_a	164.343 Å
Unit-cell length b length_b	164.343 Å
Unit-cell length c length_c	164.343 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	24

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	24.500 Å
R factor r_factor	0.1595
R_work r_work	0.1585
R_free r_free	0.1789

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) COLLECTED AT 1.280 ANGSTROM

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

Phosphohydrolase

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

2zoa__assembly_1__model_1

2zoa__assembly_1__model_1 | I(q)

2zoa__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) COLLECTED AT 1.280 ANGSTROM

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

Phosphohydrolase

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

2zoa__assembly_1__model_1

2zoa__assembly_1__model_1 | I(q)

2zoa__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)