SAXSdb — 9rlf

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1. Structure Basics

entry_id	9rlf
deposition_date	2025-06-16
title	LolCDE complex with Pal lipoprotein
keywords	Gram-negative, envelope biogenesis, outer membrane protein, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	45.71 Å
rg_electron	45.16 Å
i0	275875000.00
molecular_weight	140140.0 kDa
excluded_volume	177300 Å³
envelope_volume	248010 Å³
shell_volume	48331 Å³
envelope_diameter	144.7 Å
shell_rg	46.40 Å
envelope_rg	44.47 Å
shape_rg	45.18 Å
total_rg	45.16 Å
total_atoms	9840
n_residues	1280
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	134.7 Å
rg_real	46.08 Å
rg_real_error	0.89 Å
i0_real	2.7590e+08
i0_real_error	4.8820e+06
rg_reciprocal	45.72 Å
i0_reciprocal	275700000.0000
total_estimate	0.7909
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.5 Å
skewness	0.365
kurtosis	-0.893
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	28650000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.758; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	9840

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	26306.2 kDa
ec_number	7.6.2.-
mutation	C-terminal His tag (GSHHHHHH)
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,F

MNKILLQCDNLCKRYQEGSVQTDVLHNVSFSVGEGEMMAIVGSSGSGKSTLLHLLGGLDTPTSGDVIFNGQPMSKLSSAAKAELRNQKLGFIYQFHHLLPDFTALENVAMPLLIGKKKPAEINSRALEMLKAVGLDHRANHRPSELSGGERQRVAIARALVNNPRLVLADEPTGNLDARNADSIFQLLGELNRLQGTAFLVVTHDLQLAKRMSRQLEMRDGRLTAELSLMGAEGSHHHHH

Source

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

Entity 4 polymer

description	Peptidoglycan-associated lipoprotein
formula_weight	17821.6 kDa
mutation	C-terminal GS linker strep II tag (GSWSHPQFEK)
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

CSSNKNASNDGSEGMLGAGTGMDANGGNGNMSSEEQARLQMQQLQQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVYGSWSHPQFEK

Source

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

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

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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	triclinic

resolution	3.17 Å
resolution_method	—
num_particles	89446

fit	/app/data/saxs_computation/rl/9rlf/9rlf.fit
pddf	/app/data/pr_computation/rl/9rlf/9rlf.pr.out
profile	/app/data/saxs_computation/rl/9rlf/9rlf.dat

LolCDE complex with Pal lipoprotein

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)