SAXSdb — 9c27

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

Capsid protein 2

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 × 60 PDB declaration: 60-meric（60） Consistent with protein copy count	Chain A； UniProt 1–554	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.20 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–554	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.20 Å
3	Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–554	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.20 Å
4	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–554	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.20 Å
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–554	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.20 Å

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.

Other PDB	Difference from Current Entry 9C27	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9C2T Infectious B19V capsid Deposited 2024-05-31	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 2–554（553 aa） Chain B 2–554（553 aa） Chain C 2–554（553 aa） Chain D 2–554（553 aa） Chain E 2–554（553 aa） Chain F 2–554（553 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9C4F Infectious B19V capsid Deposited 2024-06-04	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–554（554 aa） Chain B 1–554（554 aa） Chain C 1–554（554 aa） Chain D 1–554（554 aa） Chain E 1–554（554 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q784T0_PAVHB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–554； UniProt 1–554

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	9c27
Deposition date deposition_date	2024-05-30
Structure title title	Infectious B19V capsid
Keywords keywords	B19, Virion, Capsid, VIRUS; VIRUS
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	29.04 Å
Radius of gyration Rg (electron density) rg_electron	28.22 Å
Forward intensity I(0) i0	52744500.00
Molecular weight molecular_weight	56896.0 kDa
Excluded volume excluded_volume	71226 Å³
Envelope volume envelope_volume	98787 Å³
Hydration-shell volume shell_volume	30187 Å³
Envelope diameter envelope_diameter	123.5 Å
Shell Rg shell_rg	33.85 Å
Envelope Rg envelope_rg	29.71 Å
Shape Rg shape_rg	28.17 Å
Total Rg total_rg	28.98 Å
Total atoms total_atoms	4021
Residues n_residues	517
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	117.3 Å
Rg (real space) rg_real	29.23 Å
Rg uncertainty (real space) rg_real_error	1.43 Å
I(0) (real space) i0_real	5.2740e+07
I(0) uncertainty (real space) i0_real_error	9.1390e+05
Rg (reciprocal space) rg_reciprocal	29.14 Å
I(0) (reciprocal space) i0_reciprocal	52740000.0000
Solution quality estimate total_estimate	0.7549
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.0 Å
Skewness Skewness skewness	0.642
Kurtosis Kurtosis kurtosis	0.483
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8202000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.439; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.519; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	16458

Description description	Capsid protein 2
Molecular weight formula_weight	60916.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4021

Infectious B19V capsid

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

Capsid protein 2

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/c2/9c27/9c27.fit
pddf	/app/data/pr_computation/c2/9c27/9c27.pr.out
profile	/app/data/saxs_computation/c2/9c27/9c27.dat