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11kc

Cryo-EM determined structure of designed nanoparticle O43-TM

Method: ELECTRON MICROSCOPY D_max: 326.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11kc
deposition_date	2026-02-27
title	Cryo-EM determined structure of designed nanoparticle O43-TM
keywords	De Novo, Membrane, Hydrophobic, Designed, Two Component, Octahedral, Micelle, DE NOVO PROTEIN; DE NOVO 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	91.92 Å
rg_electron	91.03 Å
i0	10255600000.00
molecular_weight	872890.0 kDa
excluded_volume	1094700 Å³
envelope_volume	2514500 Å³
shell_volume	241540 Å³
envelope_diameter	305.9 Å
shell_rg	93.90 Å
envelope_rg	80.46 Å
shape_rg	91.08 Å
total_rg	90.90 Å
total_atoms	114096
n_residues	9864
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	326.6 Å
rg_real	94.73 Å
rg_real_error	2.00 Å
i0_real	1.0210e+10
i0_real_error	2.5850e+08
rg_reciprocal	94.84 Å
i0_reciprocal	10350000000.0000
total_estimate	0.8544
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	134.5 Å
skewness	0.411
kurtosis	0.780
angular_range	— – 0.0850 Å⁻¹
current_alpha	1.0470
highest_alpha	2668000000.0000
n_real_points	18
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.519; Stabil: 0.928; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.872

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Designed nanoparticle O43-TM
formula_weight	25101.2 kDa
src_method	man
entity_count	24

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
atom_count	114096

SKDTEDSRKIWRTIMLLLVFAILLSAIIWYQITTNPDTSQIATLLSMQLLLIALMLVVIALLLSRQTEQVAESIRRDVSALAYVMLGLLLSLLNRLSLAAEAYKKAIELDPNDALAWLLLGSVLEKLKRLDEAAEAYKKAIELKPNDASAWKELGKVLEKLGRLDEAADAYAEALRLDPDDTEAWKELGKVLEKLGMEEAAAMAKKAAKLLDPNDGSLEHHHHHH

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 polymer

description	Designed nanoparticle O43-B
formula_weight	23244.1 kDa
src_method	man
entity_count	24

Polymer

type	polypeptide(L)
strand_id	a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x

MEELFKKHKIVAVLRANSVEEAKEKAQAVFEGGVHLIEITFTVPDADTVIKELSKLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVDLDNVCEWFKAGVLAVGVGEALVDGEPRAVKIAAIAFRAVIKGCGCTEGSLEHHHHHH

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
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	4.07 Å
resolution_method	—
num_particles	42340

fit	/app/data/saxs_computation/1k/11kc/11kc.fit
pddf	/app/data/pr_computation/1k/11kc/11kc.pr.out
profile	/app/data/saxs_computation/1k/11kc/11kc.dat

Cryo-EM determined structure of designed nanoparticle O43-TM

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)