SAXSdb — 7ek9

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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	(4R)-2-METHYLPENTANE-2,4-DIOL × 3 (4S)-2-METHYL-2,4-PENTANEDIOL × 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
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 38–160 Author chain B； PDBConstruct 1–123； UniProt 38–160 Author chain C； PDBConstruct 1–123； UniProt 38–160 Author chain D； PDBConstruct 1–123； UniProt 38–160

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	7ek9
Deposition date deposition_date	2021-04-04
Structure title title	Crystal structure of apo streptavidin at cryogenic temperature
Keywords keywords	Streptavidin, cooperative allostery, ambient temperature, cryogenic temperature, STRUCTURAL PROTEIN; STRUCTURAL 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.

7ek9__assembly_1__model_1

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

Download this curve (.dat)

7ek9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ek9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.86 Å
Rg (electron density)	21.77 Å
Total Rg	22.72 Å
Atom count	3604
Residues	482
Excluded volume	62931 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ek9__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	12981.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4462

EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPS

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	(4R)-2-METHYLPENTANE-2,4-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 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	617

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7ek9A01
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	7ek9B01
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	7ek9C01
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	7ek9D01
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	46.373 Å
Unit-cell length b length_b	85.946 Å
Unit-cell length c length_c	58.188 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.100 Å
Low-resolution limit resolution_low	17.896 Å
R factor r_factor	0.1602
R_work r_work	0.1587
R_free r_free	0.1871

Crystal structure of apo streptavidin at cryogenic temperature

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

7ek9__assembly_1__model_1

7ek9__assembly_1__model_1 | I(q)

7ek9__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of apo streptavidin at cryogenic temperature

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

7ek9__assembly_1__model_1

7ek9__assembly_1__model_1 | I(q)

7ek9__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)