SAXSdb — 1yu0

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

Major Tropism Determinant (Mtd-P1)

Bordetella phage BPP-1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	CALCIUM ION × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q775D6_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–381； UniProt 1–381

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	1yu0
Deposition date deposition_date	2005-02-11
Structure title title	Major Tropism Determinant P1 Variant
Keywords keywords	C-type Lectin, Beta Sandwich, Beta Prism, variability, diversity-generating retroelement, Viral protein; VIRAL 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.

1yu0__assembly_1__model_1

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

Download this curve (.dat)

1yu0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yu0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.58 Å
Rg (electron density)	29.52 Å
Total Rg	30.24 Å
Atom count	8276
Residues	1128
Excluded volume	145020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yu0__assembly_1__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	Major Tropism Determinant (Mtd-P1)
Molecular weight formula_weight	39557.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3248

MSTAVQFRGGTTAQHATFTGAAREITVDTDKNTVVVHDGATAGGFPLARHDLVKTAFIKADKSAVAFTRTGNATASIKAGTIVEVNGKLVQFTADTAITMPALTAGTDYAIYVCDDGTVRADSNFSAPTGYTSTTARKVGGFHYAPGSNAAAQAGGNTTAQINEYSLWDIKFRPAALDPRGMTLVAGAFWADIYLLGVNHLTDGTSKYNVTIADGSASPKKSTKFGGDGSAAYSDGAWYNFAEVMTHHGKRLPNYNEFQALAFGTTEATSSGGTDVPTTGVNGTGATSAWNIFTSKWGVVQASGCLWTWGNEFGGVNGASEYTANTGGRGSVYAQPAAALFGGAWNGTSLSGSRAALWYSGPSFSFAFFGARGVCDHLILE

Source Source

Source organism organism	Bordetella phage BPP-1
NCBI taxonomy ID ncbi_taxonomy_id	194699
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	488

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1yu0a1
Class class	b — All beta proteins
Fold Fold fold	b.163 — Pseudo beta-prism I
Superfamily Superfamily superfamily	b.163.1 — Bacteriophage trimeric proteins domain
Family Family family	b.163.1.1 — Mtd domain-like

Domain ID domain_id	d1yu0a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.8 — Mtd variable domain

CATH v4.4 (3 domains)

Domain ID domain_id	1yu0A01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	10 — Seminal Fluid Protein PDC-109 (Domain B)
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1yu0A02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	20 — Tail fiber receptor-binding protein
Homologous superfamily homologous superfamily	10 — Tail fiber receptor-binding protein

Domain ID domain_id	1yu0A03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1580 — paralog of FGE (formylglycine-generating enzyme)
Homologous superfamily homologous superfamily	10 — paralog of FGE (formylglycine-generating enzyme)

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Unit-cell length a length_a	92.258 Å
Unit-cell length b length_b	92.258 Å
Unit-cell length c length_c	102.231 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.560 Å
Low-resolution limit resolution_low	20.330 Å
R factor r_factor	0.1284
R_work r_work	0.1275
R_free r_free	0.1448

Major Tropism Determinant P1 Variant

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

Major Tropism Determinant (Mtd-P1)

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

1yu0__assembly_1__model_1

1yu0__assembly_1__model_1 | I(q)

1yu0__assembly_1__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 (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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Major Tropism Determinant P1 Variant

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

Major Tropism Determinant (Mtd-P1)

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

1yu0__assembly_1__model_1

1yu0__assembly_1__model_1 | I(q)

1yu0__assembly_1__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 (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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)