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9vc6

Cryo-EM structure of Bacillus halodurans ComEC

Method: ELECTRON MICROSCOPY D_max: 96.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vc6
deposition_date	2025-06-05
title	Cryo-EM structure of Bacillus halodurans 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	30.33 Å
rg_electron	29.56 Å
i0	108835000.00
molecular_weight	89860.0 kDa
excluded_volume	115710 Å³
envelope_volume	145780 Å³
shell_volume	40676 Å³
envelope_diameter	101.0 Å
shell_rg	37.17 Å
envelope_rg	29.40 Å
shape_rg	29.58 Å
total_rg	30.28 Å
total_atoms	6346
n_residues	774
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	96.4 Å
rg_real	30.27 Å
rg_real_error	0.65 Å
i0_real	1.0880e+08
i0_real_error	1.6960e+06
rg_reciprocal	30.30 Å
i0_reciprocal	108800000.0000
total_estimate	0.8918
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.2 Å
skewness	0.304
kurtosis	-0.347
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	25090000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.859

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Competence protein ComEC
formula_weight	92434.0 kDa
mutation	H579A, D581A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6346

MGHHHHHHHHHHSSGLEVLFQGPGGGSGTGSGSGSMASRIIFLFSLLIMLGLATGLRGFSASFGFLTFLLLLIILCQQYRRFQLLFLAILLFLCAWLYGVVQERQNETQLNPLDQNVGGTLISDPELDGDQFSVTVKTTDGEKVLIRGRVQVEAEKDKLEMMQIGMFCSFVGQLEIPNEPTNPYQFNYRQFLYNNRIHWIFRTDLSQWQCSDQPTTLFIKVKRWRSERLQDIYDLASDETAGLIAAFVYGDRSELDDELLSAYQSLGVIHLLAVSGLHVGLVVAAVFYLLIRLGVTRERAYELLLLFLPFYAIVAGAAPSVVREVGMTITVLLALRFQKRLAPVIVLSIVAVLYIIIEPYAIFTLGFQLSFLTTCALLLSSSTLLQAINRPLLSLLKVTFLAQLISMPVILYHFFELPVLSVPLNLLFVPIVSFVLLPLSFFVASSLLIHPAVAELPLFILEIIVPIVHQLLLVLNEQSFATVVIGKPSLNSVFLMMISLIIGWAWLERKEPFKAWGAFSVVLFLIGWQIYSPYWSNEAVVTMIDVGQGDSFLIELPRREAIYMIDTGGWVTYGEMEPWQERRNTRDIGEQVLTPILKGKGIQGIDKLILTHGAEAHFGGAEGLVRSIKVDEIVYGYKHGEYTEREREVLSALKKAGASIRFVKSGDQWVIGSSSFRVLSPFGDEEELNDQSVVVYAVIEGVRFLFTGDLEEVGEKRLLEFHGNLKADVLKVGHHGSATSTTDPFLEAVHPVVALISAGRNNLYGHPNQDVLAALEQYEAFVLRTDLHGAVKLTIRDGAIYARVMTTDGSGSPSRLEEELRRRLTEP

Source

organism	Halalkalibacterium halodurans C-125
ncbi_taxonomy_id	272558
host_organism	Escherichia coli

Entity 2 non-polymer

description	Lauryl Maltose Neopentyl Glycol
formula_weight	1005.2 kDa
src_method	syn
entity_count	3

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	2.71 Å
resolution_method	—
num_particles	251581

fit	/app/data/saxs_computation/vc/9vc6/9vc6.fit
pddf	/app/data/pr_computation/vc/9vc6/9vc6.pr.out
profile	/app/data/saxs_computation/vc/9vc6/9vc6.dat