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- PDB-9htu: Structure of endolysin PlyP100 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 9htu
TitleStructure of endolysin PlyP100 catalytic domain
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsHYDROLASE / PlyP100 / endolysin
Function / homologysymbiont-mediated cytolysis of host cell / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / defense response to bacterium / N-acetylmuramoyl-L-alanine amidase
Function and homology information
Biological speciesListeria phage LP-125 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsScaletti Hutchinson, E. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural and functional insights into Listeriamonocytogenes phage endolysin PlyP100: A promising food safety tool.
Authors: Bateman, K.R. / Scaletti Hutchinson, E. / Widmalm, G. / Miller, M.J. / Stenmark, P.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1185
Polymers19,7641
Non-polymers3544
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-53 kcal/mol
Surface area9080 Å2
Unit cell
Length a, b, c (Å)37.306, 65.864, 96.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-acetylmuramoyl-L-alanine amidase


Mass: 19764.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria phage LP-125 (virus) / Gene: LP125_088 / Production host: Escherichia coli (E. coli) / References: UniProt: S4U9Y8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium sulfate, 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→96.51 Å / Num. obs: 22719 / % possible obs: 99.6 % / Redundancy: 12 % / CC1/2: 0.978 / Net I/σ(I): 10.8
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 1239 / CC1/2: 0.798

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.3 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.1 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18268 1151 5.1 %RANDOM
Rwork0.15158 ---
obs0.15317 21506 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.367 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å2-0 Å20 Å2
2---0.5 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 16 308 1719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131476
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161346
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.6292005
X-RAY DIFFRACTIONr_angle_other_deg1.5551.5893109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3075187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46923.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85915243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.186153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
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_it1.4141.717739
X-RAY DIFFRACTIONr_mcbond_other1.4141.717738
X-RAY DIFFRACTIONr_mcangle_it1.7882.565929
X-RAY DIFFRACTIONr_mcangle_other1.7882.565930
X-RAY DIFFRACTIONr_scbond_it2.9392.011737
X-RAY DIFFRACTIONr_scbond_other2.8341.982726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1722.8361059
X-RAY DIFFRACTIONr_long_range_B_refined5.99622.9291831
X-RAY DIFFRACTIONr_long_range_B_other5.44421.1251712
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 85 -
Rwork0.228 1484 -
obs--95.03 %

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