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9ugq

Cryo-EM structure of ClassIII Salivaricin modification enzyme SalKC in the presence of SalA

Method: ELECTRON MICROSCOPY D_max: 125.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ugq
deposition_date	2025-04-13
title	Cryo-EM structure of ClassIII Salivaricin modification enzyme SalKC in the presence of SalA
keywords	Lanthibiotic, RiPPs, LanKC, CryoEM, Antimicrobial peptides, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL 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	39.91 Å
rg_electron	39.28 Å
i0	520368000.00
molecular_weight	193180.0 kDa
excluded_volume	244180 Å³
envelope_volume	319130 Å³
shell_volume	65735 Å³
envelope_diameter	125.2 Å
shell_rg	46.91 Å
envelope_rg	38.28 Å
shape_rg	39.28 Å
total_rg	39.73 Å
total_atoms	13674
n_residues	1732
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	125.7 Å
rg_real	39.74 Å
rg_real_error	0.70 Å
i0_real	5.2040e+08
i0_real_error	7.5930e+06
rg_reciprocal	39.91 Å
i0_reciprocal	520500000.0000
total_estimate	0.8261
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	53.4 Å
skewness	0.102
kurtosis	-0.524
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0001
highest_alpha	102000000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	SalKC
formula_weight	100188.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	13674

MQYDFSLKDPLFFTLTDDDLTDFSSKYSAPLPYDWHELSNNSEWVNQYPIGFTTERQGWKVHISSDYKHSHEVLEVVSKVCHEFRVVFKYLKTEKVFVLRNGKNIDRGYSGKFITCYPNIESLEGFLKELERKLKGYTGPYILSDRRWREAPIYLRYGVFRESIPELEGNLKSDELLVSGKIIKDIRSPKFIIPEGLEIPEFLEKWLKDIKGDEKSEFPFTIESAIRFSNCGGIYNATLSSSNKKIILREARPYTGLDFSGEYSTERMKSERRALTILKDIDGIPNVFWYGKLWEHNFLGVEKMDGIPLNHWLTKNYPLYDSKGKEKYLYRAKNILKQLISIVERAHKHSVYHQDIHFGNILIDRSDRLSLIDWEQVRFDNSKMVEQKMAAPGYGSWIDDYPSKIDWYGVKQIAHYLYFPLIEQTSLVLGYDQQTFKVAHRNFVEMGYSDTDIKNMEVIINALDNKCSTFDNLSEKKILKPCLNNLVINSKADINDFASRLGKGLLTISDEWKRKYKNKRIFPVHYYGLKINQGIAFSDLGILLSYKKLIDLLSDKVDNSYEEIKNLAIQTAIAKFRDDSPGLLDGMSGTIWIIHELGEKQLAIDLFRKYYSEMLRKSSEKNIYSGTAGILLVGLYLISQHNDLSIKELIISDMNLFADNYLFNPSDFCKVGVGDTNSNDPYEADSGLLFGHTGIGWLFGEAYRYTKNSKFLKCLNLAIESELVAYEKDDFDRLQYNQGKRLLPYLSTGSAGLLLLISRNKEFLQNSVLNNCHYLEKAVSPNFCVFPGIANGMCGLFLSKNLYKSNINYVQQCKELIRCLETYLCVVEDGFALAGDSGLKLTTDISTGTAGIILTLVSLRNGKLELLPSVQ

Source

organism	Streptococcus salivarius
ncbi_taxonomy_id	1304
host_organism	Escherichia coli

Entity 2 polymer

description	SalA
formula_weight	1792.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MLEEVLKLQLMDAKE

Source

organism	Streptococcus salivarius
ncbi_taxonomy_id	1304
host_organism	Escherichia coli

Entity 3 non-polymer

description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
formula_weight	523.2 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

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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	—

fit	/app/data/saxs_computation/ug/9ugq/9ugq.fit
pddf	/app/data/pr_computation/ug/9ugq/9ugq.pr.out
profile	/app/data/saxs_computation/ug/9ugq/9ugq.dat

Cryo-EM structure of ClassIII Salivaricin modification enzyme SalKC in the presence of SalA

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)