SAXSdb — 9vyg

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1. Structure Basics

entry_id	9vyg
deposition_date	2025-07-21
title	Cyanopodophage Pan3 tail complex
keywords	Cyanophage, Virus, Tail, Adaptor, Nozzle, Needle, Tailspike, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	58.62 Å
rg_electron	57.84 Å
i0	5053550000.00
molecular_weight	587180.0 kDa
excluded_volume	728810 Å³
envelope_volume	1095900 Å³
shell_volume	150940 Å³
envelope_diameter	195.1 Å
shell_rg	66.11 Å
envelope_rg	56.20 Å
shape_rg	57.89 Å
total_rg	57.86 Å
total_atoms	41366
n_residues	5440
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	186.3 Å
rg_real	58.21 Å
rg_real_error	1.31 Å
i0_real	5.0540e+09
i0_real_error	1.0500e+08
rg_reciprocal	58.94 Å
i0_reciprocal	5059000000.0000
total_estimate	0.8773
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	82.8 Å
skewness	0.044
kurtosis	-0.462
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	368000000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.872

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Adaptor protein
formula_weight	19930.5 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	41366

MATCRDIVTRALHMAAIVPLGKDPKAAEGQLGLELLQGLYDGWFAGGMFGRLTDVYTDTAYTAKEGERVTVDGGTLTIPDTFEDTDTGLTRAPRELAAIVEINAGNITNRVWCGGEWQECSGLTLNDEAPLSKRDAMGLSCLLALHMAEAFGTQIGPMTARRGLQFQGSVSYKLGSTQPDASGVYY

Entity 2 polymer

description	Stabilization protein
formula_weight	48753.9 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	M,N,O,P,Q,R

MDLAYGTGAYARTRGNLPELPLVNLFVEATRSDQRGVVLQSRKGLVEDAEVGTGPIRGVFRKDGVLGGAEFVVSDDELYEDGVSLGTINGTGPVSFAAIEDELLVCAGESIWSYDGTTLDEVTFPDGADVTKVAYSSGYFIALRAGTGQWYFSALYDGTSWDGLDFATAESEPDALLDIVVLDGNPVFFGTQSVEFWSATGDPDIPFAPIQNRTFEQGIFATGCAVAIDNSFFWVGADKIVYRNDAVPVAVADDGIVERATGSTDLRLFLLIDERHKFVCLRGDTFTMAFDITTNEWCEFQSYGRTNFRCGPDMGDDETGIIWRFEGYSDNGGVLERRFRAGATLPGPFRVNRLRLICEVGTTPNLSGEYADPVIEMRASDDAGNTWGIWEGETLGAQGNYRQRVEWRALGLFDDPGMLFEHRMTAPVSFRVTAVTVNGELGGRSR

Entity 3 polymer

description	Needle protein
formula_weight	7375.2 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	S,T,U

VSLRLDRLQRGVPIVDGQGRPNTQYQNLWQRTVKALEADSAATADILQELADQLALIVAAQAAADAAQA

Entity 4 polymer

description	Tail spike protein
formula_weight	13478.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	m

MAAQLFYLPFRPMLDANALAVPGAKLYFYATGTTTKQPVYTSSALTTQLPNPVVANAAGKFPAIYLNDALTYRCYIEDADGNELADSDPYLASIADELTDELQDVVDAVEADRVAAANSATAAATSAA

Entity 5 polymer

description	Tail spike protein
formula_weight	13576.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	n

AAQLFYLPFRPMLDANALAVPGAKLYFYATGTTTKQPVYTSSALTTQLPNPVVANAAGKFPAIYLNDALTYRCYIEDADGNELADSDPYLASIADELTDELQDVVDAVEADRVAAANSATAAATSAAQT

Entity 6 polymer

description	Tail spike protein
formula_weight	13276.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	o

AAQLFYLPFRPMLDANALAVPGAKLYFYATGTTTKQPVYTSSALTTQLPNPVVANAAGKFPAIYLNDALTYRCYIEDADGNELADSDPYLASIADELTDELQDVVDAVEADRVAAANSATAAATSA

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.50 Å
resolution_method	—
num_particles	119673

fit	/app/data/saxs_computation/vy/9vyg/9vyg.fit
pddf	/app/data/pr_computation/vy/9vyg/9vyg.pr.out
profile	/app/data/saxs_computation/vy/9vyg/9vyg.dat

Cyanopodophage Pan3 tail complex

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)