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- PDB-9jzo: Crystal structure of PHICD111_20024_EAD. -

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Basic information

Entry
Database: PDB / ID: 9jzo
TitleCrystal structure of PHICD111_20024_EAD.
ComponentsEndolysine
KeywordsANTIBIOTIC / Endolysin
Function / homology: / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / Endolysine
Function and homology information
Biological speciesClostridium phage phiCD111 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHwang, J.S. / Seo, M.D.
Funding support1items
OrganizationGrant numberCountry
Other governmentGRRCAjou2023-B03
CitationJournal: J Glob Antimicrob Resist / Year: 2025
Title: In vitro characterization of PHICD111_20024_EAD as an engineered endolysin against Clostridioides difficile.
Authors: Park, J. / Yoo, S. / An, J. / Cho, Y. / Park, K. / Hwang, J. / Chun, S.I. / Kang, N.J. / Seo, M.D. / Yoon, H.
History
DepositionOct 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endolysine
B: Endolysine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3754
Polymers38,2442
Non-polymers1312
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size chromatography shows that it is a homodimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-72 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.630, 43.100, 54.200
Angle α, β, γ (deg.)112.970, 90.110, 118.180
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Endolysine


Mass: 19121.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium phage phiCD111 (virus) / Gene: PHICD111_20024 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A8WHU0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.01 Å3/Da / Density % sol: 38.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES (pH 7.5), 0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350, and 50% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.4→26.06 Å / Num. obs: 50347 / % possible obs: 85.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.86 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.51
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 5085 / CC1/2: 0.982

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.4→26.06 Å / SU ML: 0.113 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 18.89
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1946 2518 5 %
Rwork0.1602 47829 -
obs0.1619 50347 85.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.55 Å2
Refinement stepCycle: LAST / Resolution: 1.4→26.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 2 334 3010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522714
X-RAY DIFFRACTIONf_angle_d0.83663664
X-RAY DIFFRACTIONf_chiral_restr0.0753428
X-RAY DIFFRACTIONf_plane_restr0.0053458
X-RAY DIFFRACTIONf_dihedral_angle_d5.9222370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.25431390.19242650X-RAY DIFFRACTION85.47
1.43-1.460.21181430.17692716X-RAY DIFFRACTION88.4
1.46-1.490.21581470.16722775X-RAY DIFFRACTION88.22
1.49-1.520.16791380.16092623X-RAY DIFFRACTION86.47
1.52-1.560.20651370.16022616X-RAY DIFFRACTION84.27
1.56-1.60.19261340.15472535X-RAY DIFFRACTION81.47
1.6-1.650.20321430.15312725X-RAY DIFFRACTION88.55
1.65-1.70.18381450.15552756X-RAY DIFFRACTION88.85
1.7-1.760.18891410.16042682X-RAY DIFFRACTION87.56
1.76-1.830.19251380.15812619X-RAY DIFFRACTION84.6
1.83-1.920.17271340.16492545X-RAY DIFFRACTION81.95
1.92-2.020.20431460.16312771X-RAY DIFFRACTION89.2
2.02-2.150.17511420.16462705X-RAY DIFFRACTION87.98
2.15-2.310.19531400.16192654X-RAY DIFFRACTION85.63
2.31-2.540.21041370.16762596X-RAY DIFFRACTION83.58
2.54-2.910.22471440.1762733X-RAY DIFFRACTION88.2
2.91-3.670.20471320.1582506X-RAY DIFFRACTION81.29
3.67-26.060.16661380.14372622X-RAY DIFFRACTION84.64

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