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11ci

Staphylococcus aureus-specific lysin L1-3 (LysM-CHAP) covalently complexed to Pep1a-CMK substrate mimic

Method: X-RAY DIFFRACTION D_max: 62.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11ci
deposition_date	2026-02-17
last_revision	2026-05-06
title	Staphylococcus aureus-specific lysin L1-3 (LysM-CHAP) 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	18.08 Å
rg_electron	17.24 Å
i0	15602400.00
molecular_weight	20356.0 kDa
excluded_volume	19892 Å³
envelope_volume	31043 Å³
shell_volume	15618 Å³
envelope_diameter	64.4 Å
shell_rg	22.87 Å
envelope_rg	17.57 Å
shape_rg	17.22 Å
total_rg	17.98 Å
total_atoms	1551
n_residues	189
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	62.3 Å
rg_real	18.09 Å
rg_real_error	0.46 Å
i0_real	1.5600e+07
i0_real_error	2.1580e+05
rg_reciprocal	18.09 Å
i0_reciprocal	15600000.0000
total_estimate	0.7844
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	21.9 Å
skewness	0.408
kurtosis	-0.157
angular_range	— – 0.4400 Å⁻¹
current_alpha	0.0000
highest_alpha	4852000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Probable cell wall hydrolase LytN
formula_weight	24122.0 kDa
ec_number	3.-.-.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1555

REAPKTQIYTVKKGDTLSAIALKYKTTVSNIQNTNNIANPNLIFIGQKLKVPMTPLVEPKPETVSGNEKSNSGSSTLNYLKSLEGKGWDFDGSFGWQCFDLVNVYWNHLYGHGLKGYYAKDIPYANNFNSEAKIYHNTPTFKAEPGDLVVFSGRYGGGYGHTAIVLNGNYDGNLQKFQSLDQNWNGGGERKQEVAHKVVHNYENDMIFIRPFKKA

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	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4

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6. Citations (1)

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length_a	66.994 Å
length_b	135.046 Å
length_c	57.626 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.830 Å
resolution_low	30.010 Å
r_factor	0.2570
r_work	0.2559
r_free	0.2776

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

Staphylococcus aureus-specific lysin L1-3 (LysM-CHAP) covalently complexed to Pep1a-CMK substrate mimic

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

Diffraction