SAXSdb — 1c8n

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

COAT PROTEIN

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 180 PDB declaration: 180-MERIC（180） Consistent with protein copy count	Chain A； UniProt 1–269 Chain B； UniProt 1–269 Chain C； UniProt 1–269	Not recorded	CA CALCIUM ION × 300	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.25 Å R-free 0.273
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–269 Chain B； UniProt 1–269 Chain C； UniProt 1–269	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.25 Å R-free 0.273
3	Protein homooligomer Homooligomer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain A； UniProt 1–269 Chain B； UniProt 1–269 Chain C； UniProt 1–269	Not recorded	CA CALCIUM ION × 25	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.25 Å R-free 0.273
4	Protein homooligomer Homooligomer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count	Chain A； UniProt 1–269 Chain B； UniProt 1–269 Chain C； UniProt 1–269	Not recorded	CA CALCIUM ION × 30	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.25 Å R-free 0.273
5	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–269 Chain B； UniProt 1–269 Chain C； UniProt 1–269	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.25 Å R-free 0.273
6	Protein homooligomer Homooligomer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain A； UniProt 1–269 Chain B； UniProt 1–269 Chain C； UniProt 1–269	Not recorded	CA CALCIUM ION × 25	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.25 Å R-free 0.273

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q9IPS9_9TOMB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–276； UniProt 1–269 Author chain B； PDBConstruct 8–276； UniProt 1–269 Author chain C； PDBConstruct 8–276； UniProt 1–269

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	1c8n
Deposition date deposition_date	2000-05-20
Structure title title	TOBACCO NECROSIS VIRUS
Keywords keywords	VIRUS, Icosahedral virus; VIRUS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.37 Å
Radius of gyration Rg (electron density) rg_electron	28.02 Å
Forward intensity I(0) i0	62621600.00
Molecular weight molecular_weight	64357.0 kDa
Excluded volume excluded_volume	81318 Å³
Envelope volume envelope_volume	96985 Å³
Hydration-shell volume shell_volume	29866 Å³
Envelope diameter envelope_diameter	96.7 Å
Shell Rg shell_rg	34.25 Å
Envelope Rg envelope_rg	28.62 Å
Shape Rg shape_rg	28.00 Å
Total Rg total_rg	28.71 Å
Total atoms total_atoms	4532
Residues n_residues	597
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	90.7 Å
Rg (real space) rg_real	28.42 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	6.2620e+07
I(0) uncertainty (real space) i0_real_error	9.2990e+05
Rg (reciprocal space) rg_reciprocal	28.41 Å
I(0) (reciprocal space) i0_reciprocal	62620000.0000
Solution quality estimate total_estimate	0.9002
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.325
Kurtosis Kurtosis kurtosis	-0.548
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8398000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.935

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1c8na_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.7 — Tombusviridae-like VP

Domain ID domain_id	d1c8nb_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.7 — Tombusviridae-like VP

Domain ID domain_id	d1c8nc_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.7 — Tombusviridae-like VP

CATH v4.4 (3 domains)

Domain ID domain_id	1c8nA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1c8nB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1c8nC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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8. Citations (4)

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Unit-cell length a length_a	336.400 Å
Unit-cell length b length_b	336.400 Å
Unit-cell length c length_c	336.400 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	360

Space group space_group	P 42 3 2
Space-group number int_tables_number	208
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2530
R_work r_work	0.2530
R_free r_free	0.2730

Description description	COAT PROTEIN
Molecular weight formula_weight	29985.2 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4724

TOBACCO NECROSIS VIRUS

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

COAT PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	192

fit	/app/data/saxs_computation/c8/1c8n/1c8n.fit
pddf	/app/data/pr_computation/c8/1c8n/1c8n.pr.out
profile	/app/data/saxs_computation/c8/1c8n/1c8n.dat