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- PDB-9dje: T4 Lysozyme T109H/G113H -

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Basic information

Entry
Database: PDB / ID: 9dje
TitleT4 Lysozyme T109H/G113H
ComponentsEndolysin
KeywordsHYDROLASE / Hydrolase (O-Glycosyl) / double histidine mutation / dHis motif / lysozyme
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Endolysin
Similarity search - Component
Biological speciesTequatrovirus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsBesaw, J.E. / Ernst, O.P.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2023-05764 Canada
Other privateMitacs IT17088
CitationJournal: Structure / Year: 2026
Title: Structural characterization of the Cu(II)-NTA spin label on alpha-helices by X-ray crystallography and electron paramagnetic resonance
Authors: Besaw, J.E. / Reichenwallner, J. / Chen, E.Y. / Hermet-Teesalu, P. / Tregubenko, A. / Kim, K. / Morizumi, T. / Ustav Jr., M. / Ernst, O.P.
History
DepositionSep 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4088
Polymers18,7471
Non-polymers6627
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.381, 59.381, 95.273
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

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Components

#1: Protein Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 18746.500 Da / Num. of mol.: 1 / Mutation: T109H, G113H, C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tequatrovirus T4 / Gene: e, T4Tp126 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D9IEF7, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Protein: 0.33 mM T4 lysozyme mutant. Precipitant: 2.2 M NaH2PO4/K2HPO4, pH 6.6, 150 mM NaCl, 100 mM 1,6-hexanediol, 3% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.62→28.35 Å / Num. obs: 25380 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 16.22 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.3
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1823 / CC1/2: 0.835 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→28.35 Å / SU ML: 0.1484 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.5418
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1842 2009 7.93 %
Rwork0.1623 23335 -
obs0.1641 25344 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.36 Å2
Refinement stepCycle: LAST / Resolution: 1.62→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 38 152 1491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311397
X-RAY DIFFRACTIONf_angle_d1.25061871
X-RAY DIFFRACTIONf_chiral_restr0.0735202
X-RAY DIFFRACTIONf_plane_restr0.0097239
X-RAY DIFFRACTIONf_dihedral_angle_d15.5765541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.26121370.2031627X-RAY DIFFRACTION98.38
1.66-1.70.22961440.18391641X-RAY DIFFRACTION100
1.7-1.750.22591360.17481634X-RAY DIFFRACTION100
1.75-1.810.18641430.16911643X-RAY DIFFRACTION100
1.81-1.880.18641440.15971649X-RAY DIFFRACTION100
1.88-1.950.20051390.14881632X-RAY DIFFRACTION100
1.95-2.040.17541430.14741688X-RAY DIFFRACTION100
2.04-2.150.13761390.13251644X-RAY DIFFRACTION100
2.15-2.280.1571480.13971650X-RAY DIFFRACTION100
2.28-2.460.17661400.1521673X-RAY DIFFRACTION100
2.46-2.710.20081480.16061677X-RAY DIFFRACTION100
2.71-3.10.1921430.15361674X-RAY DIFFRACTION100
3.1-3.90.15741480.16151708X-RAY DIFFRACTION100
3.9-28.350.20091570.18441795X-RAY DIFFRACTION99.95

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