SAXSdb — 3by1

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

58 kd capsid protein

Norwalk virus

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 homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q83884_9CALI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–313； UniProt 218–530

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	3by1
Deposition date deposition_date	2008-01-15
Structure title title	Unliganded Norvalk Virus P domain
Keywords keywords	Norwalk Virus P domain, 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.

3by1__assembly_1__model_1

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

Download this curve (.dat)

3by1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3by1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.29 Å
Rg (electron density)	19.19 Å
Total Rg	20.02 Å
Atom count	2114
Residues	280
Excluded volume	37481 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3by1__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3by1__assembly_2__model_1`	dimeric （2）	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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3by1A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	510 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Homologous superfamily homologous superfamily	10 — Positive stranded ssRNA viruses

Domain ID domain_id	3by1A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	120 — Positive stranded ssRNA viruses

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Unit-cell length a length_a	83.749 Å
Unit-cell length b length_b	82.952 Å
Unit-cell length c length_c	102.742 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	8

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.690 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2045
R_free r_free	0.2532

Description description	58 kd capsid protein
Molecular weight formula_weight	33497.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2303

Unliganded Norvalk Virus P domain

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

58 kd capsid protein

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

3by1__assembly_1__model_1

3by1__assembly_1__model_1 | I(q)

3by1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Norwalk virus
NCBI taxonomy ID ncbi_taxonomy_id	11983
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	189

Unliganded Norvalk Virus P domain

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

58 kd capsid protein

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

3by1__assembly_1__model_1

3by1__assembly_1__model_1 | I(q)

3by1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)