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- PDB-11cg: CHAP domain of Staphylococcus aureus-specific lysin L2 -

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Basic information

Entry
Database: PDB / ID: 11cg
TitleCHAP domain of Staphylococcus aureus-specific lysin L2
ComponentsCHAP domain of lysin L2
KeywordsHYDROLASE / lysin / CHAP / enzyme / peptidoglycan / bacteria / phage / LysM / endopeptidase
Function / homologyTHIOCYANATE ION
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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: CHAP domain of lysin L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,90613
Polymers16,5241
Non-polymers38112
Water1,802100
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)50.990, 71.660, 85.460
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 CHAP domain of lysin L2


Mass: 16524.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 3350, 0.2 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.15→33.04 Å / Num. obs: 52726 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.025 / Net I/σ(I): 19.9
Reflection shellResolution: 1.15→1.18 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3989 / CC1/2: 0.791 / Rpim(I) all: 0.403

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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: 1.15→33.04 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.556 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22664 2860 5.1 %RANDOM
Rwork0.21409 ---
obs0.21474 52726 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.816 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.15→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 18 100 1216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0121136
X-RAY DIFFRACTIONr_bond_other_d0.0010.016993
X-RAY DIFFRACTIONr_angle_refined_deg0.9491.7961530
X-RAY DIFFRACTIONr_angle_other_deg0.3771.772274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.52353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.19210168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0530.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
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_it0.4751.595557
X-RAY DIFFRACTIONr_mcbond_other0.4641.592554
X-RAY DIFFRACTIONr_mcangle_it0.8362.861689
X-RAY DIFFRACTIONr_mcangle_other0.8352.86690
X-RAY DIFFRACTIONr_scbond_it0.4611.642579
X-RAY DIFFRACTIONr_scbond_other0.4591.639577
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7982.983839
X-RAY DIFFRACTIONr_long_range_B_refined2.51317.871357
X-RAY DIFFRACTIONr_long_range_B_other2.36517.611335
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 200 -
Rwork0.294 3779 -
obs--98.08 %

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