SAXSdb — 1y55

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

Avidin-related protein 4/5

Gallus gallus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	BIOTIN × 4 FORMIC ACID × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AVR4_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–126； UniProt 25–150 Author chain Y； PDBConstruct 1–126； UniProt 25–150

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	1y55
Deposition date deposition_date	2004-12-02
Structure title title	Crystal structure of the C122S mutant of E. Coli expressed avidin related protein 4 (AVR4)-biotin complex
Keywords keywords	avidin, streptavidin, biotin, avidin related molecule, high affinity, thermostability, 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.

1y55__assembly_1__model_1

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

Download this curve (.dat)

1y55__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y55__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.73 Å
Rg (electron density)	21.57 Å
Total Rg	22.56 Å
Atom count	3876
Residues	480
Excluded volume	68657 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y55__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Avidin-related protein 4/5
Molecular weight formula_weight	14158.9 kDa
Mutation mutation	C122S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y
Atom count atom_count	2260

ARKCSLTGKWTNNLGSIMTIRAVNSRGEFTGTYLTAVADNPGNITLSPLLGIQHKRASQPTFGFTVHWNFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDISYDWKATRVGYNNFTRLSTVEE

Source Source

Source organism organism	Gallus gallus
Common name common_name	chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BIOTIN
Molecular weight formula_weight	244.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	240

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1y55x1
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.1 — Avidin/streptavidin
Family Family family	b.61.1.1 — Avidin/streptavidin

Domain ID domain_id	d1y55x2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1y55y1
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.1 — Avidin/streptavidin
Family Family family	b.61.1.1 — Avidin/streptavidin

Domain ID domain_id	d1y55y2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1y55X00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	1y55Y00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

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Unit-cell length a length_a	78.173 Å
Unit-cell length b length_b	78.173 Å
Unit-cell length c length_c	110.260 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.000 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1657
R_work r_work	0.1651
R_free r_free	0.1766

Crystal structure of the C122S mutant of E. Coli expressed avidin related protein 4 (AVR4)-biotin complex

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

Avidin-related protein 4/5

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

1y55__assembly_1__model_1

1y55__assembly_1__model_1 | I(q)

1y55__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 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the C122S mutant of E. Coli expressed avidin related protein 4 (AVR4)-biotin complex

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

Avidin-related protein 4/5

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

1y55__assembly_1__model_1

1y55__assembly_1__model_1 | I(q)

1y55__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 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)