SAXSdb — 9wjr

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1. Structure Basics

entry_id	9wjr
deposition_date	2025-08-31
title	Cryo-EM structure of the L. garvieae Man-PTS
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	41.59 Å
rg_electron	40.65 Å
i0	461492000.00
molecular_weight	192760.0 kDa
excluded_volume	248450 Å³
envelope_volume	329960 Å³
shell_volume	67738 Å³
envelope_diameter	127.4 Å
shell_rg	46.38 Å
envelope_rg	39.81 Å
shape_rg	40.66 Å
total_rg	40.96 Å
total_atoms	13608
n_residues	1821
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	127.0 Å
rg_real	41.37 Å
rg_real_error	0.78 Å
i0_real	4.6150e+08
i0_real_error	7.6500e+06
rg_reciprocal	41.59 Å
i0_reciprocal	461600000.0000
total_estimate	0.8361
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	56.8 Å
skewness	0.029
kurtosis	-0.644
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	44860000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Mannose/fructose/sorbose family PTS transporter subunit IIC
formula_weight	27177.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	Y,F,S
atom_count	13608

MSIISIILVLIFAFLAGLEGILDQWQFHQPIIACSLIGIATGHMAAGIILGGSLQMIALGWANVGAAVAPDAALASVASAILMVQGGNFDLTHITGVIVPAAILLATAGLVLTTLVRFLSVGIVHLADAAAEKGSYSGVAGWHMFALLLQGLRIAIPAAIILAIPAETVTAALNAIPDWVSKGLAVGGGMVVVVGYAMVINLMATKELWPFFFLGFVLAPLSSITLIGMGILGVVIALIYLNLSNTAGNGGTASSSGDPIGDILNDY

Source

organism	Lactococcus garvieae
ncbi_taxonomy_id	1363
host_organism	Lactococcus phage phiL47

Entity 2 polymer

description	PTS mannose transporter subunit IID
formula_weight	39453.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	Z,G,T

MENTNKKFSLSKNTRLSVMFRSMFLQGSWNYERMQNLGFLYSIIPALKQFYKPGSEEAKEALKRHMEFFNTHPYVAAPIVGVTLALEEEIANGVEIDEAAIQGVKVGMMGPLAGIGDPVFWFTVRPIVGAIAASLATGGSIIAPIFFFVVWNAIRIAFLWYTQEFGYKQGTAITSDLGGGMLQQITKGASILGMFILGVLIQRWVNISFTGPNAMLPSKPLADGAYVGEWIDKAGKVVVQGAQTGTTGDGVAKFDWLDQAGNGVGNGVAGQGGFAHYVTVDQLNTVDGSTLHNILGQVSSGLGLSPEQTQSLQDVFNSLIPGFIALLLTFLVLWILRKWKNKNAPLFIIIGMFVLGIVLHVAGLA

Source

organism	Lactococcus garvieae
ncbi_taxonomy_id	1363
host_organism	Lactococcus phage phiL47

Entity 3 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	2.87 Å
resolution_method	—
num_particles	876434

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

Cryo-EM structure of the L. garvieae Man-PTS

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)