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9qgm

Cryo-EM structure of the PlPVC1 central spike, 3-fold symmetrized (C3), in extended state

Method: ELECTRON MICROSCOPY D_max: 135.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qgm
deposition_date	2025-03-14
title	Cryo-EM structure of the PlPVC1 central spike, 3-fold symmetrized (C3), in extended state
keywords	Contractile injection system, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
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	40.10 Å
rg_electron	39.70 Å
i0	505403000.00
molecular_weight	184130.0 kDa
excluded_volume	231290 Å³
envelope_volume	307020 Å³
shell_volume	65856 Å³
envelope_diameter	142.5 Å
shell_rg	44.48 Å
envelope_rg	39.63 Å
shape_rg	39.66 Å
total_rg	40.12 Å
total_atoms	12963
n_residues	1665
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	135.0 Å
rg_real	40.25 Å
rg_real_error	1.06 Å
i0_real	5.0540e+08
i0_real_error	8.5000e+06
rg_reciprocal	40.11 Å
i0_reciprocal	505300000.0000
total_estimate	0.8232
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.5 Å
skewness	0.590
kurtosis	0.157
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	132700000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.497

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
formula_weight	58964.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	8A,8B,8C
atom_count	12963

MKIPEITIKISGKTLNQFTAINLTVNHYINGIPSVNITLGIAGDANYIFDAKAQAELANCRPNNELIVQIQKTILFKGIIVRQALKFKGQDSLMTLTAKHPLQKLTDGLHSQLFSKQSDEAIIKKLFSQAGIQTTIKQAPQLKTVHEQMVQFRCNDWTFLKSRLIATNTWLLPGNEVVTLITPKALNQSTVHTIHQSTNDQDIVLFEANLQWDNQRSPKTVSVQSWDITQQKLSQTIQVKNSGLGSNKLAVDSITTLTNQDWQWVFNYPLDNEQAKYLAQGIMDNLRSDNVSGSFEVEGDSCYQPGDVLALNGFGQGMDGQGIITGVSQIINQRQGWRTRLTLGMPPDAEQAVPPVKELHVGIVEKYQPDSQSLGRIPVKIPALNLTNSVLFARLGKPYASHESGFCFYPEPGDEVIIGFFECDPRFPVILGSMHNPKNKAPVEPSEKNPMKTLVIKQGDHQQALVFNNQDKTVALNSGKNTLSLQQDKDITLNSANNLITNAQEIKIQAEKSLSASGKSGVDIKGAKINLTQ

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 2 polymer

description	Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
formula_weight	6577.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	6A,6B,6C

MTVEIKELIIQAKVTDSASDLLSPRTLAQEALDNARLIEMVKQEVLDALREAGGRYELN

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

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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	2.82 Å
resolution_method	—
num_particles	47836

fit	/app/data/saxs_computation/qg/9qgm/9qgm.fit
pddf	/app/data/pr_computation/qg/9qgm/9qgm.pr.out
profile	/app/data/saxs_computation/qg/9qgm/9qgm.dat

Cryo-EM structure of the PlPVC1 central spike, 3-fold symmetrized (C3), in extended state

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)