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11ch

CHAP domain of Staphylococcus aureus-specific lysin L1 covalently complexed to Pep1a-CMK substrate mimic

Method: X-RAY DIFFRACTION D_max: 48.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11ch
deposition_date	2026-02-17
last_revision	2026-05-06
title	CHAP domain of Staphylococcus aureus-specific lysin L1 covalently complexed to Pep1a-CMK substrate mimic
keywords	lysin, CHAP, enzyme, peptidoglycan, bacteria, phage, LysM, endopeptidase, inhibitor, substrate, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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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	15.32 Å
rg_electron	14.17 Å
i0	9909980.00
molecular_weight	16112.0 kDa
excluded_volume	15856 Å³
envelope_volume	23316 Å³
shell_volume	13654 Å³
envelope_diameter	48.3 Å
shell_rg	20.37 Å
envelope_rg	14.50 Å
shape_rg	14.13 Å
total_rg	15.16 Å
total_atoms	1222
n_residues	142
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	48.2 Å
rg_real	15.20 Å
rg_real_error	0.26 Å
i0_real	9.9100e+06
i0_real_error	1.1710e+05
rg_reciprocal	15.21 Å
i0_reciprocal	9910000.0000
total_estimate	0.8902
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	19.5 Å
skewness	0.117
kurtosis	-0.411
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	2644000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Probable cell wall hydrolase LytN
formula_weight	16480.2 kDa
ec_number	3.-.-.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1376

PNSGSSTLNYLKSLEGKGWDFDGSFGWQCFDLVNVYWNHLYGHGLKGDYAKDIPYANNFNSEAKIYHNTPTFKAEPGDLVVFSGRFGGGYGHTAIVLNGNYDGNLQKFQSLDQNWNGGGERKQEVAHKVVHNYENDMIFIRPFKKA

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 2 non-polymer

description	;N~2~-acetyl-N~6~-{(4M)-3-carboxy-4-[(10aR)-6-hydroxy-3-oxo-4,10a-dihydro-3H-xanthen-9-yl]benzene-1-carbonyl}-D-lysyl-L-alanyl-D-alpha-glutaminyl-N-[(2R)-3-oxobutan-2-yl]-L-lysinamide ;
formula_weight	943.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	THIOCYANATE ION
formula_weight	58.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	130

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6. Citations (1)

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length_a	66.800 Å
length_b	66.800 Å
length_c	67.310 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 42 21 2
int_tables_number	94
crystal_system	—

resolution	1.090 Å
resolution_low	47.230 Å
r_factor	0.2319
r_work	0.2308
r_free	0.2518

fit	/app/data/saxs_computation/1c/11ch/11ch.fit
pddf	/app/data/pr_computation/1c/11ch/11ch.pr.out
profile	/app/data/saxs_computation/1c/11ch/11ch.dat