SAXSdb — 5ii9

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

Egg-lysin

Haliotis rufescens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELYS_HALRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–138； UniProt 19–154 Author chain B； PDBConstruct 3–138； UniProt 19–154 Author chain C； PDBConstruct 3–138； UniProt 19–154 Author chain D； PDBConstruct 3–138； UniProt 19–154 Author chain E； PDBConstruct 3–138； UniProt 19–154 Author chain F； PDBConstruct 3–138； UniProt 19–154

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	5ii9
Deposition date deposition_date	2016-03-01
Structure title title	Monoclinic crystal structure of red abalone lysin at 2.11 A resolution
Keywords keywords	;CELL ADHESION, FERTILIZATION, EGG-SPERM INTERACTION, GAMETE RECOGNITION, EGG-BINDING PROTEIN, ACROSOMAL PROTEIN, EGG COAT PENETRATION ;; CELL ADHESION
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.

5ii9__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5ii9__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ii9__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	17.10 Å
Rg (electron density)	16.23 Å
Total Rg	17.30 Å
Atom count	2234
Residues	131
Excluded volume	19994 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ii9__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ii9__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5ii9__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5ii9__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5ii9__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5ii9__assembly_6__model_1`	monomeric （1）	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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5ii9a_
Class class	a — All alpha proteins
Fold Fold fold	a.19 — Fertilization protein
Superfamily Superfamily superfamily	a.19.1 — Fertilization protein
Family Family family	a.19.1.1 — Fertilization protein

Domain ID domain_id	d5ii9b_
Class class	a — All alpha proteins
Fold Fold fold	a.19 — Fertilization protein
Superfamily Superfamily superfamily	a.19.1 — Fertilization protein
Family Family family	a.19.1.1 — Fertilization protein

Domain ID domain_id	d5ii9c_
Class class	a — All alpha proteins
Fold Fold fold	a.19 — Fertilization protein
Superfamily Superfamily superfamily	a.19.1 — Fertilization protein
Family Family family	a.19.1.1 — Fertilization protein

Domain ID domain_id	d5ii9d_
Class class	a — All alpha proteins
Fold Fold fold	a.19 — Fertilization protein
Superfamily Superfamily superfamily	a.19.1 — Fertilization protein
Family Family family	a.19.1.1 — Fertilization protein

Domain ID domain_id	d5ii9e_
Class class	a — All alpha proteins
Fold Fold fold	a.19 — Fertilization protein
Superfamily Superfamily superfamily	a.19.1 — Fertilization protein
Family Family family	a.19.1.1 — Fertilization protein

Domain ID domain_id	d5ii9f_
Class class	a — All alpha proteins
Fold Fold fold	a.19 — Fertilization protein
Superfamily Superfamily superfamily	a.19.1 — Fertilization protein
Family Family family	a.19.1.1 — Fertilization protein

CATH v4.4 (6 domains)

Domain ID domain_id	5ii9A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	10 — Fertilization protein

Domain ID domain_id	5ii9B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	10 — Fertilization protein

Domain ID domain_id	5ii9C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	10 — Fertilization protein

Domain ID domain_id	5ii9D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	10 — Fertilization protein

Domain ID domain_id	5ii9E00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	10 — Fertilization protein

Domain ID domain_id	5ii9F00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	150 — Lysin
Homologous superfamily homologous superfamily	10 — Fertilization protein

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Unit-cell length a length_a	39.190 Å
Unit-cell length b length_b	69.340 Å
Unit-cell length c length_c	182.750 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.110 Å
Low-resolution limit resolution_low	27.340 Å
R factor r_factor	0.1980
R_work r_work	0.1960
R_free r_free	0.2290

Description description	Egg-lysin
Molecular weight formula_weight	16483.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	14034

Monoclinic crystal structure of red abalone lysin at 2.11 A resolution

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

Egg-lysin

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

5ii9__assembly_5__model_1

5ii9__assembly_5__model_1 | I(q)

5ii9__assembly_5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (4)

Source organism organism	Haliotis rufescens
Common name common_name	California red abalone
NCBI taxonomy ID ncbi_taxonomy_id	6454
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	515

Monoclinic crystal structure of red abalone lysin at 2.11 A resolution

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

Egg-lysin

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

5ii9__assembly_5__model_1

5ii9__assembly_5__model_1 | I(q)

5ii9__assembly_5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (4)