SAXSdb — 2z8f

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

Galacto-N-biose/lacto-N-biose I transporter substrate-binding protein

Bifidobacterium longum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 1 ZINC ION × 2 SODIUM ION × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 1 ZINC ION × 3 SODIUM ION × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
3	Other combination	Homooligomer	Protein 4 其他Polymer 4	beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 4 ZINC ION × 10 SODIUM ION × 6 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8W790_BIFLO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–412； UniProt 28–438 Author chain B； PDBConstruct 2–412； UniProt 28–438

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	2z8f
Deposition date deposition_date	2007-09-05
Structure title title	The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-tetraose
Keywords keywords	ABC TRANSPORTER, MUCIN CORE-1, HUMAN MILK OLIGOSACCHALIDE, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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.

2z8f__assembly_3__model_1

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

Download this curve (.dat)

2z8f__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2z8f__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	39.24 Å
Rg (electron density)	38.71 Å
Total Rg	39.03 Å
Atom count	12294
Residues	1600
Excluded volume	217620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2z8f__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2z8f__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2z8f__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 (6)

Entity 1 Entity 1 polymer

Description description	Galacto-N-biose/lacto-N-biose I transporter substrate-binding protein
Molecular weight formula_weight	43972.5 kDa
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	7119

MDTAGDTKTTDDGGVVNITYMHRLPDSEGMTLVNDIVAKWNKQHPDIQVKATKFDGKASDMIKKLETDVKSGEAPDLAQVGYAELPEVFTKGLLQDVTQYAEQYKNDFASGPYSLVQVGGKAYGLPQDTGPLVYFYNKAEFEKLGITEIPQTADEFIAAAKTAAAAGKYIMSYQPDEAGNMISGLAGASGGWYKVKGDSWVVNTETDGSKATADFYQQLLDAKAATTNPRWDPSFDASIKDGSLIGTVAAAWEAPLFMTSSGGTGSGEWQVAQLGDWFGNAGKTGPDGGSAVAVLKNSKHPKEAMEFLDWFNTQVPDLVSQGLVPAATTEDAETPSEWSTFFGGQDIMKEFKTANNNMGDFTYMPGFSAVAAKMNETAAKATDGSGKVADIFSDAQTTSVDTLKNFGLSVSE

Source Source

Source organism organism	Bifidobacterium longum
NCBI taxonomy ID ncbi_taxonomy_id	216816
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
Molecular weight formula_weight	707.6 kDa
Source method src_method	man
Copy count entity_count	2

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	5

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	972

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2z8fA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	2z8fA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	2z8fB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	2z8fB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

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Unit-cell length a length_a	106.151 Å
Unit-cell length b length_b	143.050 Å
Unit-cell length c length_c	113.736 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	30.270 Å
R factor r_factor	0.1803
R_work r_work	0.1786
R_free r_free	0.2140

The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-tetraose

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

Galacto-N-biose/lacto-N-biose I transporter substrate-binding protein

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

2z8f__assembly_3__model_1

2z8f__assembly_3__model_1 | I(q)

2z8f__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-tetraose

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

Galacto-N-biose/lacto-N-biose I transporter substrate-binding protein

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

2z8f__assembly_3__model_1

2z8f__assembly_3__model_1 | I(q)

2z8f__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)