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9vc9

Cryo-EM structure of Shewanella decolorationis ComEC

Method: ELECTRON MICROSCOPY D_max: 100.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vc9
deposition_date	2025-06-05
title	Cryo-EM structure of Shewanella decolorationis ComEC
keywords	Competence, DNA channel, Membrane protein, Hydrolase; MEMBRANE 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	29.24 Å
rg_electron	28.59 Å
i0	86028700.00
molecular_weight	79245.0 kDa
excluded_volume	101840 Å³
envelope_volume	123290 Å³
shell_volume	36213 Å³
envelope_diameter	111.6 Å
shell_rg	35.46 Å
envelope_rg	28.63 Å
shape_rg	28.59 Å
total_rg	29.32 Å
total_atoms	5608
n_residues	704
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	100.8 Å
rg_real	29.24 Å
rg_real_error	0.71 Å
i0_real	8.6030e+07
i0_real_error	1.3220e+06
rg_reciprocal	29.24 Å
i0_reciprocal	86030000.0000
total_estimate	0.8704
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	98.9 Å
skewness	0.392
kurtosis	-0.187
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	19710000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.943

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Dna internalization-related competence protein rec2
formula_weight	89670.2 kDa
mutation	D577A, D579A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5608

MGHHHHHHHHHHSSGLEVLFQGPGGGSGTGSGSGSMNGFIFGFSATLLSAMLWPSLLPISYLPYLCLGALVLFKKASTLSGALFAVFWLTGFCFILSRQDLPLSLQPVQVRGEIISLVSQNSDWVSFDIIVDKPNLIFWPRAKLRLTWQSPEAVQVGQVWSFTLMPKSISSVLNQGGYNEQKQLISQHIVGKGRVIHAQLLTTHFSLRNHLISQLSPKLSTFAQGDILLALILGDKQLIPASKWQALRQTGTGHLVAISGLHLSVITAWVYICTLFLLSRFAAHPSRRNLVIALLLAGGSALFYSYLAGFAVSTQRALVMILLIMLLSLLRRYSSAWDRLLFALFIVLLFDPLACLSAGFWLSFCALAIILYTLESAPRIQPAEGKATFRAKARGRLAQFWSIQWRLSLVLGLVQAVFFGGLSVHSLWMNMLVVPWFSLVVIPLSMLAFILWWLGTFFGQAWFGLFHLADFTVLPYGKLLELSGNLPVHWHSVSDTLLGASLCVLLALILWRYLPHHSRYGLWHLPITLLFIPATLVFFPRMTEPSSPQWTLHLLDVGQGLAVVIEQDRRALIYDTGAAFGEDFSYSERVIIPFLSSKGLALVDYIVVSHGANAHAGGAEVLSKAYPRANWITDVAHLEGMPCLPQQIQWQQLRLSFISPQTAKGGNNASCVLRIDDGVHSLLLSGDIEKETEAVLIEQALKGAELKSQVLIAPHHGSRTSSTPAFIDAVAPELVLFPAGLNNRYGFPKPDVVARYQARNIDYFTTGREGQISVSFAAGRLEVKTYRRDLAPFWYNRLFRFGDLINPE

Source

organism	Shewanella decolorationis
ncbi_taxonomy_id	256839
host_organism	Escherichia coli

Entity 2 non-polymer

description	Lauryl Maltose Neopentyl Glycol
formula_weight	1005.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

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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	2.77 Å
resolution_method	—
num_particles	226637

fit	/app/data/saxs_computation/vc/9vc9/9vc9.fit
pddf	/app/data/pr_computation/vc/9vc9/9vc9.pr.out
profile	/app/data/saxs_computation/vc/9vc9/9vc9.dat