2ed6

Crystal Structure of Envelope Protein VP28 from White Spot Syndrome Virus (WSSV)

Method: X-RAY DIFFRACTION

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

25kDa structural protein VP25

Shrimp white spot syndrome virus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9ICB7_WSSV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–170； UniProt 32–201 Author chain B； PDBConstruct 1–170； UniProt 32–201 Author chain C； PDBConstruct 1–170； UniProt 32–201 Author chain D； PDBConstruct 1–170； UniProt 32–201 Author chain E； PDBConstruct 1–170； UniProt 32–201 Author chain F； PDBConstruct 1–170； UniProt 32–201 Author chain G； PDBConstruct 1–170； UniProt 32–201 Author chain H； PDBConstruct 1–170； UniProt 32–201 Author chain I； PDBConstruct 1–170； UniProt 32–201 Author chain J； PDBConstruct 1–170； UniProt 32–201 Author chain K； PDBConstruct 1–170； UniProt 32–201 Author chain L； PDBConstruct 1–170； UniProt 32–201

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	2ed6
Deposition date deposition_date	2007-02-14
Structure title title	Crystal Structure of Envelope Protein VP28 from White Spot Syndrome Virus (WSSV)
Keywords keywords	beta barrel, N-terminal helix protruding region, 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.

2ed6__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ed6__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ed6__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	23.55 Å
Rg (electron density)	22.50 Å
Total Rg	23.43 Å
Atom count	3864
Residues	510
Excluded volume	68426 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ed6__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ed6__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ed6__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2ed6__assembly_4__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 (2)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2ed6a1
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6b_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6c_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6d_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6e_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6f_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6g_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6h_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6i_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6j_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6k_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

Domain ID domain_id	d2ed6l_
Class class	b — All beta proteins
Fold Fold fold	b.170 — WSSV envelope protein-like
Superfamily Superfamily superfamily	b.170.1 — WSSV envelope protein-like
Family Family family	b.170.1.1 — WSSV envelope protein-like

CATH v4.4 (12 domains)

Domain ID domain_id	2ed6A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6F01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6I01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6J01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6K01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

Domain ID domain_id	2ed6L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2770 — WSSV envelope protein-like

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Unit-cell length a length_a	105.330 Å
Unit-cell length b length_b	106.710 Å
Unit-cell length c length_c	200.370 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	48

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.2480
R_work r_work	0.2480
R_free r_free	0.2810

Description description	25kDa structural protein VP25
Molecular weight formula_weight	18389.5 kDa
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	16843

Crystal Structure of Envelope Protein VP28 from White Spot Syndrome Virus (WSSV)

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

25kDa structural protein VP25

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

2ed6__assembly_2__model_1

2ed6__assembly_2__model_1 | I(q)

2ed6__assembly_2__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Shrimp white spot syndrome virus
NCBI taxonomy ID ncbi_taxonomy_id	92652
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	1387

Crystal Structure of Envelope Protein VP28 from White Spot Syndrome Virus (WSSV)

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

25kDa structural protein VP25

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

2ed6__assembly_2__model_1

2ed6__assembly_2__model_1 | I(q)

2ed6__assembly_2__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)