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9q8n

Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 16)

Method: ELECTRON MICROSCOPY D_max: 87.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q8n
deposition_date	2025-02-25
title	Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 16)
keywords	Lipid transport, Outer membrane protein, MEMBRANE PROTEIN; 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	28.24 Å
rg_electron	27.50 Å
i0	229886000.00
molecular_weight	79960.0 kDa
excluded_volume	77046 Å³
envelope_volume	136150 Å³
shell_volume	40261 Å³
envelope_diameter	91.6 Å
shell_rg	35.98 Å
envelope_rg	27.12 Å
shape_rg	27.47 Å
total_rg	28.14 Å
total_atoms	6048
n_residues	729
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	87.4 Å
rg_real	28.03 Å
rg_real_error	0.45 Å
i0_real	2.2990e+08
i0_real_error	3.1910e+06
rg_reciprocal	28.10 Å
i0_reciprocal	229900000.0000
total_estimate	0.9018
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.9 Å
skewness	0.124
kurtosis	-0.482
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	18980000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.985

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	LPS-assembly protein LptD
formula_weight	87135.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6062

ADLASQCMLGVPSYDRPLVQGDTNDLPVTINADHAKGDYPDDAVFTGSVDIMQGNSRLQADEVQLHQKEAPGQPEPVRTVDALGNVHYDDNQVILKGPKGWANLNTKDTNVWEGDYQMVGRQGRGKADLMKQRGENRYTILDNGSFTSCLPGSDTWSVVGSEIIHDREEQVAEIWNARFKVGPVPIFYSPYLQLPVGDKRRSGFLIPNAKYTTTNYFEFYLPYYWNIAPNMDATITPHYMHRRGNIMWENEFRYLSQAGAGLMELDYLPSDKVYEDEHPNDDSSRRWLFYWNHSGVMDQVWRFNVDYTKVSDPSYFNDFDNKYGSSTDGYATQKFSVGYAVQNFNATVSTKQFQVFSEQNTSSYSAEPQLDVNYYQNDVGPFDTRIYGQAVHFVNTRDDMPEATRVHLEPTINLPLSNNWGSINTEAKFLATHYQQTNLDWYNSRNTTKLDESVNRVMPQFKVDGKMVFERDMEMLAPGYTQTLEPRAQYLYVPYRDQSDIYNYDSSLLQSDYSGLFRDRTYGGLDRIASANQVTTGVTSRIYDDAAVERFNISVGQIYYFTESRTGDDNITWENDDKTGSLVWAGDTYWRISERWGLRGGIQYDTRLDNVATSNSSIEYRRDEDRLVQLNYHYASPEYIQATLPKYYSTAEQYKNGISQVGAVASRPIADRWSIVGAYYYDTNANKQADSMLGVQYSSCCYAIRVGYERKLNGWDNDKQHAVYDNAIGFNIELRGLSSNYGLGTQEMLRSNILPYQNTL

Source

organism	Shigella flexneri
ncbi_taxonomy_id	623
host_organism	Escherichia coli BL21

Entity 2 polymer

description	LPS-assembly lipoprotein LptE
formula_weight	17002.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

CGWHLRDTTQVPSTMKVMILDSGDPNGPLSRAVRNQLRLNGVELLDKETTRKDVPSLRLGKVSIAKDTASVFRNGQTAEYQMIMTVNATVLIPGRDIYPISAKVFRSFFDNPQMALAKDNEQDMIVKEMYDRAAEQLIRKLPSIRAADIRS

Source

organism	Shigella flexneri
ncbi_taxonomy_id	623
host_organism	Escherichia coli BL21

Entity 3 polymer

description	Compound 16 - Bicyclic Peptide Binder
formula_weight	1847.2 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

ACEWCIFWYDPKLCAX

Entity 4 non-polymer

description	DODECYL-BETA-D-MALTOSIDE
formula_weight	510.6 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	PALMITIC ACID
formula_weight	256.4 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
formula_weight	568.9 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	1,3,5-tris(2-chloroethylsulfonyl)-1,3,5-triazinane
formula_weight	466.8 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	2.540 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.54 Å
resolution_method	—
num_particles	168619

fit	/app/data/saxs_computation/q8/9q8n/9q8n.fit
pddf	/app/data/pr_computation/q8/9q8n/9q8n.pr.out
profile	/app/data/saxs_computation/q8/9q8n/9q8n.dat

Cryo-EM structure of Shigella flexneri LptDE bound by a Bicyclic peptide molecule (Compound 16)

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

Refinement

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)