SAXSdb — 9wjw

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1. Structure Basics

entry_id	9wjw
deposition_date	2025-08-31
title	Cryo-EM structure of the GarQ-lmYZ complex
keywords	;antibiotic resistance; antimicrobial peptides; mannose phosphotransferase system; Man-PTS; bacteriocins; non-pediocin-like/class IId bacteriocins; Garvicin Q; GarQ, 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	40.33 Å
rg_electron	39.53 Å
i0	406728000.00
molecular_weight	180810.0 kDa
excluded_volume	233380 Å³
envelope_volume	302220 Å³
shell_volume	63514 Å³
envelope_diameter	124.6 Å
shell_rg	45.54 Å
envelope_rg	38.87 Å
shape_rg	39.51 Å
total_rg	39.99 Å
total_atoms	12735
n_residues	1689
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	122.2 Å
rg_real	40.15 Å
rg_real_error	0.72 Å
i0_real	4.0670e+08
i0_real_error	6.4460e+06
rg_reciprocal	40.33 Å
i0_reciprocal	406800000.0000
total_estimate	0.8395
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	53.3 Å
skewness	0.032
kurtosis	-0.713
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	42950000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Mannose/fructose/sorbose family PTS transporter subunit IIC
formula_weight	27377.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	F,S,Y
atom_count	12735

MSVISIILVVLIAFLAGIEGILDEFQFHQPLIACTLIGLVTGNLTACIILGGTLQMIALGWANIGAAVAPDAALASVASAIILVLGGQGVAGIPSAIAIAIPLAVAGLFLTMIVRTLAVPIVHLMDRAAEKGNIRSVEWLHISAICMQGIRIAIPAAALLFIPADSVQSFLEAMPAWLTDGMAIGGGMVVAVGYALVINMMATKEVWPFFVIGFVVAAISQLTLIAIGALGVALALIYLNLSKMGGGNSNGGGGGNSRDPLGDILNDY

Source

organism	Listeria monocytogenes
ncbi_taxonomy_id	1639
host_organism	Escherichia coli

Entity 2 polymer

description	PTS mannose family transporter subunit IID
formula_weight	33402.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,T,Z

MAEKIELSKRDRLRVAWRSTFIQGSWNYERMQNGGWAFSMIPAIKKLYKTKEDRSSALKRHLEFFNTHPYIASPILGVTLALEEERANGAEVDDVAIQGVKVGMMGPLAGVGDPVFWFTIRPMLGALGASLALSGNILGPILFFVAWNVIRWGFMWYTQEFGYKAGSKITDDLSGGLLQDITKGASILGMFVLAALVQRWVNIQFAPIISKVKLDEGAYIDWSHLPQGAQGIKTALQQQQAGLALSEIKVTTLQNNLDNLIPGLAAVALTFLCMWLLKKKISPIIIILGLFVVGIVGHLIGLL

Source

organism	Listeria monocytogenes
ncbi_taxonomy_id	1639
host_organism	Escherichia coli

Entity 3 polymer

description	Prepeptide GarQ
formula_weight	5350.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

EYHLMNGANGYLTRVNGKYVYRVTKDPVSAVFGVISNGWGSAGAGFGPQH

Source

organism	Lactococcus garvieae
ncbi_taxonomy_id	1363
host_organism	Lactococcus phage phiL47

Entity 4 non-polymer

description	alpha-D-mannopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	3

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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	2.960 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.96 Å
resolution_method	—
num_particles	55270

fit	/app/data/saxs_computation/wj/9wjw/9wjw.fit
pddf	/app/data/pr_computation/wj/9wjw/9wjw.pr.out
profile	/app/data/saxs_computation/wj/9wjw/9wjw.dat

Cryo-EM structure of the GarQ-lmYZ complex

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)