SAXSdb — 5to2

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

Streptavidin

Streptomyces avidinii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	DI(HYDROXYETHYL)ETHER × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAV_STRAV
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 39–163 Author chain B； PDBConstruct 1–125； UniProt 39–163 Author chain C； PDBConstruct 1–125； UniProt 39–163 Author chain D； PDBConstruct 1–124； UniProt 39–162

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	5to2
Deposition date deposition_date	2016-10-16
Structure title title	Crystal structure of streptavidin with one wild type subunit and three mutated subunits (N23A/S27D/S45A)
Keywords keywords	Streptavidin, BIOTIN-BINDING PROTEIN; BIOTIN-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.

5to2__assembly_1__model_1

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

Download this curve (.dat)

5to2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5to2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.87 Å
Rg (electron density)	21.77 Å
Total Rg	22.75 Å
Atom count	3587
Residues	482
Excluded volume	62538 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5to2__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	Streptavidin
Molecular weight formula_weight	13050.1 kDa
Mutation mutation	N23A, S27D, S45A
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3907

AGITGTWYAQLGDTFIVTAGADGALTGTYEAAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAAS

Source Source

Source organism organism	Streptomyces avidinii
NCBI taxonomy ID ncbi_taxonomy_id	1895
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Streptavidin
Molecular weight formula_weight	12994.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAA

Source Source

Source organism organism	Streptomyces avidinii
NCBI taxonomy ID ncbi_taxonomy_id	1895
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	282

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5to2a_
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	d5to2b_
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	d5to2c_
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	d5to2d_
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

CATH v4.4 (4 domains)

Domain ID domain_id	5to2A00
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	5to2B00
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	5to2C00
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	5to2D00
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	44.357 Å
Unit-cell length b length_b	56.738 Å
Unit-cell length c length_c	57.435 Å
Unit-cell angle α angle_alpha	87.54 °
Unit-cell angle β angle_beta	85.89 °
Unit-cell angle γ angle_gamma	67.99 °
Molecules per unit cell Z z_pdb	3

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

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2057
R_work r_work	0.2043
R_free r_free	0.2336

Crystal structure of streptavidin with one wild type subunit and three mutated subunits (N23A/S27D/S45A)

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

Streptavidin

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

5to2__assembly_1__model_1

5to2__assembly_1__model_1 | I(q)

5to2__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of streptavidin with one wild type subunit and three mutated subunits (N23A/S27D/S45A)

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

Streptavidin

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

5to2__assembly_1__model_1

5to2__assembly_1__model_1 | I(q)

5to2__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)