SAXSdb — 11cf

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Probable cell wall hydrolase LytN

Staphylococcus aureus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 244–383	Not recorded	NA SODIUM ION × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；20 mM HEPES 7.4, 2 mM TCEP, 150 mM sodium chloride	Resolution 1.25 Å R-free 0.199
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 244–383	Not recorded	NA SODIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；20 mM HEPES 7.4, 2 mM TCEP, 150 mM sodium chloride	Resolution 1.25 Å R-free 0.199
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 244–383	Not recorded	NA SODIUM ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；20 mM HEPES 7.4, 2 mM TCEP, 150 mM sodium chloride	Resolution 1.25 Å R-free 0.199
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 244–383	Not recorded	NA SODIUM ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；20 mM HEPES 7.4, 2 mM TCEP, 150 mM sodium chloride	Resolution 1.25 Å R-free 0.199

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 11CF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11CH CHAP domain of Staphylococcus aureus-specific lysin L1 covalently complexed to Pep1a-CMK substrate mimic Deposited 2026-02-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 244–383（140 aa）	Not recorded	A1DEZ 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 × 1 NA SODIUM ION × 6 SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.4 M sodium chloride, 0.1 M sodium citrate pH 6.0	Resolution 1.09 Å R-free 0.252

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LYTN_STAAR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–146； UniProt 244–383 Author chain B； PDBConstruct 7–146； UniProt 244–383 Author chain C； PDBConstruct 7–146； UniProt 244–383 Author chain D； PDBConstruct 7–146； UniProt 244–383

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	11cf
Deposition date deposition_date	2026-02-17
最后修订 last_revision	2026-05-06
Structure title title	CHAP domain of Staphylococcus aureus-specific lysin L1
Keywords keywords	lysin, CHAP, enzyme, peptidoglycan, bacteria, phage, LysM, endopeptidase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.42 Å
Radius of gyration Rg (electron density) rg_electron	27.71 Å
Forward intensity I(0) i0	67326400.00
Molecular weight molecular_weight	64428.0 kDa
Excluded volume excluded_volume	80267 Å³
Envelope volume envelope_volume	100380 Å³
Hydration-shell volume shell_volume	30381 Å³
Envelope diameter envelope_diameter	96.3 Å
Shell Rg shell_rg	34.95 Å
Envelope Rg envelope_rg	27.09 Å
Shape Rg shape_rg	27.68 Å
Total Rg total_rg	28.52 Å
Total atoms total_atoms	4571
Residues n_residues	564
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	92.4 Å
Rg (real space) rg_real	28.33 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	6.7330e+07
I(0) uncertainty (real space) i0_real_error	1.0620e+06
Rg (reciprocal space) rg_reciprocal	28.36 Å
I(0) (reciprocal space) i0_reciprocal	67330000.0000
Solution quality estimate total_estimate	0.8964
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.6 Å
Skewness Skewness skewness	0.191
Kurtosis Kurtosis kurtosis	-0.534
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19270000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Probable cell wall hydrolase LytN
Molecular weight formula_weight	16480.2 kDa
EC 编号 ec_number	3.-.-.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5171

PNSGSSTLNYLKSLEGKGWDFDGSFGWQCFDLVNVYWNHLYGHGLKGDYAKDIPYANNFNSEAKIYHNTPTFKAEPGDLVVFSGRFGGGYGHTAIVLNGNYDGNLQKFQSLDQNWNGGGERKQEVAHKVVHNYENDMIFIRPFKKA

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	600

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8. Citations (1)

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Unit-cell length a length_a	48.120 Å
Unit-cell length b length_b	57.430 Å
Unit-cell length c length_c	63.050 Å
Unit-cell angle α angle_alpha	86.07 °
Unit-cell angle β angle_beta	85.22 °
Unit-cell angle γ angle_gamma	83.99 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.250 Å
Low-resolution limit resolution_low	36.640 Å
R factor r_factor	0.1878
R_work r_work	0.1873
R_free r_free	0.1989

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

CHAP domain of Staphylococcus aureus-specific lysin L1

1. Protein Identity and Related Structures Protein Identity & Related Structures

Probable cell wall hydrolase LytN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction