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- PDB-9dji: T4 Lysozyme R119H/Q123H -

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Basic information

Entry
Database: PDB / ID: 9dji
TitleT4 Lysozyme R119H/Q123H
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
: / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesTequatrovirus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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, 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)19,0508
Polymers18,6191
Non-polymers4307
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.149, 60.149, 96.617
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

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Components

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


Mass: 18619.334 Da / Num. of mol.: 1 / Mutation: R119H, Q123H, 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.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Protein: 0.33 mM T4 lysozyme mutant. Precipitant: 2.2 M NaH2PO4/K2HPO4, pH 6.8, 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: 1.1→28.72 Å / Num. obs: 79801 / % possible obs: 97 % / Redundancy: 10.4 % / Biso Wilson estimate: 11.36 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.2
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4996 / CC1/2: 0.791 / % possible all: 83.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→28.72 Å / SU ML: 0.0722 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.6992
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.154 2005 2.51 %
Rwork0.1427 77768 -
obs0.143 79773 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.1 Å2
Refinement stepCycle: LAST / Resolution: 1.1→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 19 288 1599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481380
X-RAY DIFFRACTIONf_angle_d0.83341868
X-RAY DIFFRACTIONf_chiral_restr0.0694203
X-RAY DIFFRACTIONf_plane_restr0.0056240
X-RAY DIFFRACTIONf_dihedral_angle_d18.7453519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.130.19571230.18714659X-RAY DIFFRACTION82.29
1.13-1.160.17771380.15295271X-RAY DIFFRACTION92.49
1.16-1.190.13971360.1315321X-RAY DIFFRACTION94.1
1.19-1.230.1381380.1255425X-RAY DIFFRACTION95.63
1.23-1.280.15411460.1235528X-RAY DIFFRACTION96.88
1.28-1.330.13151410.11985548X-RAY DIFFRACTION98.07
1.33-1.390.1181420.12145620X-RAY DIFFRACTION98.61
1.39-1.460.15261440.11765659X-RAY DIFFRACTION98.77
1.46-1.550.12591480.11925666X-RAY DIFFRACTION99.25
1.55-1.670.14451480.1185718X-RAY DIFFRACTION99.37
1.67-1.840.15881460.15075710X-RAY DIFFRACTION99.63
1.84-2.110.14991430.14465769X-RAY DIFFRACTION99.83
2.11-2.650.17021530.15515825X-RAY DIFFRACTION99.98
2.65-28.720.15661590.15086049X-RAY DIFFRACTION99.94

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