SAXSdb — 3bdf

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

Alkaline phosphatase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–450； UniProt 22–471 Author chain B； PDBConstruct 1–450； UniProt 22–471

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	3bdf
Deposition date deposition_date	2007-11-14
Structure title title	Crystal structure of metal-free E. coli alkaline phosphatase (T155V)
Keywords keywords	bacterial alkaline phosphatase, Hydrolase, Magnesium, Metal-binding, Periplasm, Phosphorylation, Zinc; 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.

3bdf__assembly_1__model_1

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

Download this curve (.dat)

3bdf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bdf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.63 Å
Rg (electron density)	27.96 Å
Total Rg	28.61 Å
Atom count	6363
Residues	866
Excluded volume	112360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bdf__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Alkaline phosphatase
Molecular weight formula_weight	48320.8 kDa
EC 编号 ec_number	3.1.3.1
Mutation mutation	T155V
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	7819

RTPEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDAVPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLKLEHHHHHH

Source Source

Source organism organism	Escherichia coli
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1222

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3bdfa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.76 — Alkaline phosphatase-like
Superfamily Superfamily superfamily	c.76.1 — Alkaline phosphatase-like
Family Family family	c.76.1.1 — Alkaline phosphatase

Domain ID domain_id	d3bdfb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.76 — Alkaline phosphatase-like
Superfamily Superfamily superfamily	c.76.1 — Alkaline phosphatase-like
Family Family family	c.76.1.1 — Alkaline phosphatase

CATH v4.4 (2 domains)

Domain ID domain_id	3bdfA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	720 — Alkaline Phosphatase, subunit A
Homologous superfamily homologous superfamily	10 — Alkaline Phosphatase, subunit A

Domain ID domain_id	3bdfB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	720 — Alkaline Phosphatase, subunit A
Homologous superfamily homologous superfamily	10 — Alkaline Phosphatase, subunit A

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Unit-cell length a length_a	55.503 Å
Unit-cell length b length_b	103.634 Å
Unit-cell length c length_c	88.550 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1630
R_work r_work	0.1620
R_free r_free	0.1840

Crystal structure of metal-free E. coli alkaline phosphatase (T155V)

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

Alkaline 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

3bdf__assembly_1__model_1

3bdf__assembly_1__model_1 | I(q)

3bdf__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of metal-free E. coli alkaline phosphatase (T155V)

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

Alkaline 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

3bdf__assembly_1__model_1

3bdf__assembly_1__model_1 | I(q)

3bdf__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)