SAXSdb — 2vty

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

PROTEIN F1

VACCINIA VIRUS

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 18–186	Fragment：RESIDUES 18-186	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.2；0.9 NACL, 50 MM NA/K PHOSPHATE PH 5.2	Resolution 2.10 Å R-free 0.207

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 2VTY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4D2L Vaccinia Virus F1L bound to Bak BH3 Deposited 2014-05-12	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 18–186（169 aa） Fragment：RESIDUES 18-186	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.18 M AMMONIUM SULFATE AND 2.25 M LICL., pH 7.5	Resolution 2.90 Å R-free 0.228
4D2M Vaccinia Virus F1L bound to Bim BH3 Deposited 2014-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 18–186（169 aa） Fragment：RESIDUES 18-186 Chain C 18–186（169 aa） Fragment：RESIDUES 18-186	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 CL CHLORIDE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；0.2M KCL, 15 % PEG400, 1.44 % MPD AND 0.1M AMMONIUM CITRATE PH 6.2.	Resolution 2.10 Å R-free 0.255

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

View Construct and Data Evidence

UniProt name	VF01_VACCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–182； UniProt 18–186

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	2vty
Deposition date deposition_date	2008-05-19
Structure title title	Vaccinia virus anti-apoptotic F1L is a novel Bcl-2-like domain swapped dimer
Keywords keywords	BCL-2, APOPTOSIS, VACCINIA VIRUS; APOPTOSIS
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	18.92 Å
Radius of gyration Rg (electron density) rg_electron	18.10 Å
Forward intensity I(0) i0	5314540.00
Molecular weight molecular_weight	16626.0 kDa
Excluded volume excluded_volume	20861 Å³
Envelope volume envelope_volume	27392 Å³
Hydration-shell volume shell_volume	13685 Å³
Envelope diameter envelope_diameter	63.1 Å
Shell Rg shell_rg	22.81 Å
Envelope Rg envelope_rg	17.90 Å
Shape Rg shape_rg	18.12 Å
Total Rg total_rg	18.91 Å
Total atoms total_atoms	1162
Residues n_residues	144
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	61.3 Å
Rg (real space) rg_real	18.86 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	5.3150e+06
I(0) uncertainty (real space) i0_real_error	7.4150e+04
Rg (reciprocal space) rg_reciprocal	18.87 Å
I(0) (reciprocal space) i0_reciprocal	5315000.0000
Solution quality estimate total_estimate	0.8992
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	60.5 Å
Skewness Skewness skewness	0.161
Kurtosis Kurtosis kurtosis	-0.358
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	311600.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.958

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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2vtyA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	437 — Apoptosis Regulator Bcl-x
Homologous superfamily homologous superfamily	10 — Blc2-like

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8. Citations (1)

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Unit-cell length a length_a	88.261 Å
Unit-cell length b length_b	88.261 Å
Unit-cell length c length_c	88.261 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	12

Space group space_group	P 2 3
Space-group number int_tables_number	195
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	88.390 Å
R factor r_factor	0.1930
R_work r_work	0.1920
R_free r_free	0.2070

Description description	PROTEIN F1
Molecular weight formula_weight	21456.2 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	1244

Vaccinia virus anti-apoptotic F1L is a novel Bcl-2-like domain swapped dimer

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

PROTEIN F1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	VACCINIA VIRUS
NCBI Class编号 ncbi_taxonomy_id	10245
宿主生物 host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

fit	/app/data/saxs_computation/vt/2vty/2vty.fit
pddf	/app/data/pr_computation/vt/2vty/2vty.pr.out
profile	/app/data/saxs_computation/vt/2vty/2vty.dat