SAXSdb — 9xro

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1. Structure Basics

entry_id	9xro
deposition_date	2025-11-19
title	LolCDE in complex with SMT-738_3
keywords	Bacterial lipoprotein transporter, LolCDE inhibitor, Cryo-EM, Allosteric conformational change, TRANSPORT PROTEIN; TRANSPORT 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	41.70 Å
rg_electron	41.71 Å
i0	304831000.00
molecular_weight	95331.0 kDa
excluded_volume	92371 Å³
envelope_volume	174180 Å³
shell_volume	38048 Å³
envelope_diameter	141.6 Å
shell_rg	42.35 Å
envelope_rg	41.50 Å
shape_rg	41.68 Å
total_rg	41.80 Å
total_atoms	7230
n_residues	957
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	141.7 Å
rg_real	42.18 Å
rg_real_error	1.53 Å
i0_real	3.0480e+08
i0_real_error	5.9850e+06
rg_reciprocal	41.71 Å
i0_reciprocal	304700000.0000
total_estimate	0.6883
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	29.8 Å
skewness	0.500
kurtosis	-0.746
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	19540000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.476; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.517; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Lipoprotein-releasing system transmembrane protein LolC
formula_weight	43295.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	7230

MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNILGLMPQAILSSEHGSLNPQQLPETAVKLDGVNRVAPITTGDVVLQSARSVAVGVMLGIDPAQKDPLTPYLVNVKQTDLEPGKYNVILGEQLASQLGVNRGDQIRVMVPSASQFTPMGRIPSQRLFNVIGTFAANSEVDGYEMLVNIEDASRLMRYPAGNITGWRLWLDEPLKVDSLSQQKLPEGSKWQDWRDRKGELFQAVRMEKNMMGLLLSLIVAVAAFNIITSLGLMVMEKQGEVAILQTQGLTPRQIMMVFMVQGASAGIIGAILGAALGALLASQLNNLMPIIGVLLDGAALPVAIEPLQVIVIALVAMAIALLSTLYPSWRAAATQPAEALRYE

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Lipoprotein-releasing system transmembrane protein LolE
formula_weight	45386.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MAMPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRILAVVPHGEIEAVDQPWTNWQEALDHVQKVPGIAAAAPYINFTGLVESGANLRAIQVKGVNPQQEQRLSALPSFVQGDAWRNFKAGEQQIIIGKGVADALKVKQGDWVSIMIPNSNPEHKLMQPKRVRLHVAGILQLSGQLDHSFAMIPLADAQQYLDMGSSVSGIALKMTDVFNANKLVRDAGEVTNSYVYIKSWIGTYGYMYRDIQMIRAIMYLAMVLVIGVACFNIVSTLVMAVKDKSGDIAVLRTLGAKDGLIRAIFVWYGLLAGLFGSLCGVIIGVVVSLQLTPIIEWIEKLIGHQFLSSDIYFIDFLPSELHWLDVFYVLVTALLLSLLASWYPARRASNIDPARVLSGQ

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	Lipoprotein-releasing system ATP-binding protein LolD
formula_weight	26576.5 kDa
ec_number	7.6.2.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MNKILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDTPTSGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPAEINSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADEPTGNLDARNADSIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSLMGAEHHHHHHHH

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

description	2-azanyl-1-[6-[2-azanyl-5-(3-methylpyridin-4-yl)-1H-imidazol-4-yl]-2,3-dihydro-1,4-benzoxazin-4-yl]-2-methyl-propan-1-one
formula_weight	392.5 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	2.880 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.88 Å
resolution_method	—
num_particles	403023

fit	/app/data/saxs_computation/xr/9xro/9xro.fit
pddf	/app/data/pr_computation/xr/9xro/9xro.pr.out
profile	/app/data/saxs_computation/xr/9xro/9xro.dat

LolCDE in complex with SMT-738_3

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)