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9vcf

Cryo-EM structure of Shewanella putrefaciens ComEC in complex with dsDNA

Method: ELECTRON MICROSCOPY D_max: 115.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vcf
deposition_date	2025-06-05
title	Cryo-EM structure of Shewanella putrefaciens ComEC in complex with dsDNA
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	31.21 Å
rg_electron	30.37 Å
i0	122060000.00
molecular_weight	87131.0 kDa
excluded_volume	108930 Å³
envelope_volume	140370 Å³
shell_volume	39113 Å³
envelope_diameter	121.6 Å
shell_rg	36.81 Å
envelope_rg	30.64 Å
shape_rg	30.30 Å
total_rg	31.15 Å
total_atoms	6112
n_residues	733
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	115.4 Å
rg_real	31.32 Å
rg_real_error	1.15 Å
i0_real	1.2210e+08
i0_real_error	1.8580e+06
rg_reciprocal	31.27 Å
i0_reciprocal	122100000.0000
total_estimate	0.6048
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	33.9 Å
skewness	0.513
kurtosis	0.060
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	17140000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.640; Stabil: 1.000; Sysdev: 0.040; Positv: 1.000; Valcen: 0.838; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA internalization-related competence protein ComEC/Rec2
formula_weight	93053.6 kDa
mutation	D577A, D579A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6112

MGHHHHHHHHHHSSGLEVLFQGPGGGSGTGSGSGSMNRFILGFSASLLSAMLWPSLPPVAYLPYLLVGALILYQKAPLCSGVLFAMLWLTVFCLGLSRQDLPVQQQPLQVRGEIISLVSQNSDWLSLDIAIIKPNLILRPRAKLRLTWKAPPDVAVGQVWLFTITPKSVSNVLNQGGYNEQKQLISQHIVGKGRVIKAELIESQPSLRNQLVSALAPQLAPLQQGDLLLALILGDKQLISSERWQMLRQTATGHLVAISGLHLSVVTAWIYAVMIFGLTRFVPHPSRRNWVFALLLSGIGAAFYAYLAGFGISTQRALVMILLLMLLSLLKRFSSPWERLLFALFMVLLIDPLACLSAGFWLSFCALAIILYTLEAAPKVHQLTNDITPLGRVRAGLLQFWSIQWRLSLGLGFVQAVLFGGISAHSLWINMLAVPWFSFVVIPIAMAGFVCWWIGTALGFSWMGLLELSNWALMPYGQLLAISGQLPIHWQVVSESVLALALCGVLGGVLWRYIPKQRLYWPWRFIVSLLFVPFLLSFLLKWLPLKSATWSMHLLDVGQGLAVVIEKEGRGLIYDTGAAFGESFSYSQRVIIPFLNAKGIREIDYVFISHSANAHAGGASALLAAYPKAQWITDVTEIAGKGCRPQQINWQDLKISIIFPQKPIAGNNGSCVVRIDDTQQRVLLTGDIEKNSEMKLLTQVKMQPTILMSQVLIAPHHGSKSSSTEAFIDAVSPELVLFPAGLGNRYGFPKPVVVDRYQARNIPHLTTGIEGQISVIFRHDSREVKTYRRDLAPFWYNRLFRFGDLINPEGSGDYKDDDDKGSPSRLEEELRRRLTEP

Source

organism	Shewanella putrefaciens
ncbi_taxonomy_id	24
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (30-MER)
formula_weight	9178.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

CCCGCAGCAATGTACAAATAACATAACAGT

Entity 3 polymer

description	DNA (30-MER)
formula_weight	9266.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

ACTGTTATGTTATTTGTACATTGCTGCGGG

Entity 4 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	3.23 Å
resolution_method	—
num_particles	42796

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

Cryo-EM structure of Shewanella putrefaciens ComEC in complex with dsDNA

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)