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- PDB-11ci: Staphylococcus aureus-specific lysin L1-3 (LysM-CHAP) covalently ... -

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Basic information

Entry
Database: PDB / ID: 11ci
TitleStaphylococcus aureus-specific lysin L1-3 (LysM-CHAP) covalently complexed to Pep1a-CMK substrate mimic
ComponentsProbable cell wall hydrolase LytN
KeywordsHYDROLASE / lysin / CHAP / enzyme / peptidoglycan / bacteria / phage / LysM / endopeptidase / inhibitor / substrate
Function / homology
Function and homology information


lytic endotransglycosylase activity / Hydrolases / cell wall organization / hydrolase activity / extracellular region
Similarity search - Function
CHAP domain profile. / CHAP domain / CHAP domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / YSIRK Gram-positive signal peptide / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
: / Probable cell wall hydrolase LytN
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsMiller, H.A. / Palowitch, G.M. / Dulberger, C.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2026
Title: Multi-dimensional optimization of a lysin towards a ribolysin against life-threatening S. aureus infections: Fc-LysM-CHAP and its strong synergy with standard of care antibiotics
Authors: Badarau, A. / Bauer, B. / Visram, Z. / Qiao, R. / Majoros-Hashempour, A. / Sollner, J. / Durica-Mitic, S. / Dunne, O.M. / Kluj, R. / Kestemont, D. / Kieninger, A.K. / Kulig, M. / Berdaguer, ...Authors: Badarau, A. / Bauer, B. / Visram, Z. / Qiao, R. / Majoros-Hashempour, A. / Sollner, J. / Durica-Mitic, S. / Dunne, O.M. / Kluj, R. / Kestemont, D. / Kieninger, A.K. / Kulig, M. / Berdaguer, R. / Schwebs, T. / Zerbs, M. / Czermak, P. / von Freyberg, M. / Schmidt, J. / Schmidberger, L. / Mayer, D. / Protano, M. / Miller, H.A. / Palowitch, G.M. / Dulberger, C.L. / Massaro, M. / Ivanisenko, N. / Jacomet, H. / Ngatcha Bakoue, D. / Oteri, F. / Sela, G. / Corsini, L.
History
DepositionFeb 17, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable cell wall hydrolase LytN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0883
Polymers24,1221
Non-polymers9662
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.994, 135.046, 57.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Probable cell wall hydrolase LytN


Mass: 24122.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: lytN, SAS1181 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G9W6, Hydrolases
#2: Chemical ChemComp-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


Mass: 943.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H58N8O13 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG MME 5000, 0.1 M TRIS pH 8.5, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.83→30.03 Å / Num. obs: 6204 / % possible obs: 99.8 % / Redundancy: 7.2 % / CC1/2: 0.971 / Rmerge(I) obs: 0.335 / Rpim(I) all: 0.194 / Net I/σ(I): 4.8
Reflection shellResolution: 2.83→2.9 Å / Rmerge(I) obs: 1.517 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 481 / CC1/2: 0.571 / Rpim(I) all: 1.755

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→30.01 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.86 / SU B: 23.121 / SU ML: 0.405 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27763 310 4.8 %RANDOM
Rwork0.25592 ---
obs0.25698 6204 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.236 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å2-0 Å20 Å2
2--6.65 Å20 Å2
3----2.83 Å2
Refinement stepCycle: 1 / Resolution: 2.83→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 1 4 1555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0121595
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161410
X-RAY DIFFRACTIONr_angle_refined_deg0.7111.7972168
X-RAY DIFFRACTIONr_angle_other_deg0.2791.7573219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3485187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5091115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.18510223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0320.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021938
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02405
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3363.667754
X-RAY DIFFRACTIONr_mcbond_other0.3363.667754
X-RAY DIFFRACTIONr_mcangle_it0.6346.59939
X-RAY DIFFRACTIONr_mcangle_other0.6346.589940
X-RAY DIFFRACTIONr_scbond_it0.4343.767841
X-RAY DIFFRACTIONr_scbond_other0.4343.767842
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8056.971230
X-RAY DIFFRACTIONr_long_range_B_refined2.14437.51772
X-RAY DIFFRACTIONr_long_range_B_other2.14337.541773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.83→2.901 Å
RfactorNum. reflection% reflection
Rfree0.288 19 -
Rwork0.385 450 -
obs--98.32 %

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