SAXSdb — 1c8h

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer 蛋白 60 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: complete icosahedral assembly	Entity 1：CANINE PARVOVIRUS CAPSID × 60 缺少 UniProt 身份时不显示参考序列区间	Entity 1Mutation：K386Q	CA CALCIUM ION × 120	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.75-1.5% PEG8000, 8 mM CaCl2, 20 mM Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å
2	Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric	Entity 1：CANINE PARVOVIRUS CAPSID × 1 缺少 UniProt 身份时不显示参考序列区间	Entity 1Mutation：K386Q	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.75-1.5% PEG8000, 8 mM CaCl2, 20 mM Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å
3	Protein homooligomer Homooligomer 蛋白 5 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: pentameric	Entity 1：CANINE PARVOVIRUS CAPSID × 5 缺少 UniProt 身份时不显示参考序列区间	Entity 1Mutation：K386Q	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.75-1.5% PEG8000, 8 mM CaCl2, 20 mM Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å
4	Protein homooligomer Homooligomer 蛋白 6 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: hexameric	Entity 1：CANINE PARVOVIRUS CAPSID × 6 缺少 UniProt 身份时不显示参考序列区间	Entity 1Mutation：K386Q	CA CALCIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.75-1.5% PEG8000, 8 mM CaCl2, 20 mM Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å
5	Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric	Entity 1：CANINE PARVOVIRUS CAPSID × 1 缺少 UniProt 身份时不显示参考序列区间	Entity 1Mutation：K386Q	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.75-1.5% PEG8000, 8 mM CaCl2, 20 mM Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å
6	Protein homooligomer Homooligomer 蛋白 120 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: 120-meric	Entity 1：CANINE PARVOVIRUS CAPSID × 120 缺少 UniProt 身份时不显示参考序列区间	Entity 1Mutation：K386Q	CA CALCIUM ION × 240	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.75-1.5% PEG8000, 8 mM CaCl2, 20 mM Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å

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	1c8h
Deposition date deposition_date	2000-05-05
Structure title title	CANINE PARVOVIRUS STRAIN D EMPTY CAPSID STRUCTURE AT PH 5.5
Keywords keywords	beta barrel, viral capsid, icosahedral symmetry, Icosahedral virus, 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	29.09 Å
Radius of gyration Rg (electron density) rg_electron	28.39 Å
Forward intensity I(0) i0	62784800.00
Molecular weight molecular_weight	61177.0 kDa
Excluded volume excluded_volume	76177 Å³
Envelope volume envelope_volume	106440 Å³
Hydration-shell volume shell_volume	32210 Å³
Envelope diameter envelope_diameter	107.0 Å
Shell Rg shell_rg	34.33 Å
Envelope Rg envelope_rg	28.85 Å
Shape Rg shape_rg	28.36 Å
Total Rg total_rg	29.13 Å
Total atoms total_atoms	4321
Residues n_residues	544
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	102.5 Å
Rg (real space) rg_real	29.18 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	6.2780e+07
I(0) uncertainty (real space) i0_real_error	1.0080e+06
Rg (reciprocal space) rg_reciprocal	29.14 Å
I(0) (reciprocal space) i0_reciprocal	62780000.0000
Solution quality estimate total_estimate	0.6311
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	0.511
Kurtosis Kurtosis kurtosis	0.096
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7167000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.927; Smooth: 0.888

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c8ha_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

CATH v4.4 (1 domains)

Domain ID domain_id	1c8hA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

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8. Citations (5)

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Unit-cell length a length_a	254.493 Å
Unit-cell length b length_b	253.601 Å
Unit-cell length c length_c	452.044 Å
Unit-cell angle α angle_alpha	77.48 °
Unit-cell angle β angle_beta	74.91 °
Unit-cell angle γ angle_gamma	69.27 °
Molecules per unit cell Z z_pdb	120

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

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	9.000 Å
R factor r_factor	0.2600
R_work r_work	—
R_free r_free	—

Description description	CANINE PARVOVIRUS CAPSID
Molecular weight formula_weight	64705.6 kDa
Mutation mutation	K386Q
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4321

CANINE PARVOVIRUS STRAIN D EMPTY CAPSID STRUCTURE AT PH 5.5

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

Assembly Composition of the Current Entry

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (5)

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	2

fit	/app/data/saxs_computation/c8/1c8h/1c8h.fit
pddf	/app/data/pr_computation/c8/1c8h/1c8h.pr.out
profile	/app/data/saxs_computation/c8/1c8h/1c8h.dat