11ci

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

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

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

Probable cell wall hydrolase LytN

Staphylococcus aureus

UniProt Q6G9W6

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 169–383 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 × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;25% PEG MME 5000, 0.1 M TRIS pH 8.5, 0.2 M lithium sulfate Resolution 2.83 Å R-free 0.278

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name LYTN_STAAS
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–215; UniProt 169–383

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.

SAXS scattering curve SAXS Profile

SAXS profile for 11ci

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 11ci
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2. Structure Basics 2. Structure Basics

Entry ID entry_id11ci
Deposition date deposition_date2026-02-17
最后修订 last_revision2026-05-06
Structure title titleStaphylococcus aureus-specific lysin L1-3 (LysM-CHAP) covalently complexed to Pep1a-CMK substrate mimic
Keywords keywordslysin, CHAP, enzyme, peptidoglycan, bacteria, phage, LysM, endopeptidase, inhibitor, substrate, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.08
Radius of gyration Rg (electron density) rg_electron17.24
Forward intensity I(0) i015602400.00
Molecular weight molecular_weight20356.0 kDa
Excluded volume excluded_volume19892 ų
Envelope volume envelope_volume31043 ų
Hydration-shell volume shell_volume15618 ų
Envelope diameter envelope_diameter64.4
Shell Rg shell_rg22.87
Envelope Rg envelope_rg17.57
Shape Rg shape_rg17.22
Total Rg total_rg17.98
Total atoms total_atoms1551
Residues n_residues189
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax62.3
Rg (real space) rg_real18.09
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real1.5600e+07
I(0) uncertainty (real space) i0_real_error2.1580e+05
Rg (reciprocal space) rg_reciprocal18.09
I(0) (reciprocal space) i0_reciprocal15600000.0000
Solution quality estimate total_estimate0.7844
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.9
Skewness Skewness skewness0.408
Kurtosis Kurtosis kurtosis-0.157
Angular range angular_range— – 0.4400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4852000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.742; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)