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- PDB-9djj: T4 Lysozyme R119H/Q123H co-crystallized with Cu(II)-NTA -

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Basic information

Entry
Database: PDB / ID: 9djj
TitleT4 Lysozyme R119H/Q123H co-crystallized with Cu(II)-NTA
ComponentsEndolysin
KeywordsHYDROLASE / Hydrolase (O-Glycosyl) / double histidine mutation / dHis-Cu(II)-NTA 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
COPPER (II) ION / HEXANE-1,6-DIOL / NITRILOTRIACETIC ACID / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesTequatrovirus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,44810
Polymers18,6191
Non-polymers8299
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.182, 60.182, 96.408
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 288 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NTA / NITRILOTRIACETIC ACID


Mass: 191.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Protein: 0.33 mM T4 lysozyme mutant, 3.3 mM Cu(II)-NTA. 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: 1.33→28.72 Å / Num. obs: 46840 / % possible obs: 99.6 % / Redundancy: 10.9 % / Biso Wilson estimate: 14.58 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 1.33→1.37 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3265 / CC1/2: 0.86 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→28.72 Å / SU ML: 0.1062 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.2999
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1748 2010 4.3 %
Rwork0.1497 44783 -
obs0.1507 46793 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.8 Å2
Refinement stepCycle: LAST / Resolution: 1.33→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 44 279 1615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591392
X-RAY DIFFRACTIONf_angle_d1.08871874
X-RAY DIFFRACTIONf_chiral_restr0.0727202
X-RAY DIFFRACTIONf_plane_restr0.0066241
X-RAY DIFFRACTIONf_dihedral_angle_d13.8146530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.360.20971330.18123006X-RAY DIFFRACTION94.92
1.36-1.40.21941420.15823164X-RAY DIFFRACTION100
1.4-1.440.17811400.15233167X-RAY DIFFRACTION100
1.44-1.490.16271430.13183173X-RAY DIFFRACTION100
1.49-1.540.15451430.12373185X-RAY DIFFRACTION100
1.54-1.60.15651420.11613177X-RAY DIFFRACTION100
1.6-1.680.16341440.12913181X-RAY DIFFRACTION100
1.68-1.770.15061460.12113158X-RAY DIFFRACTION100
1.77-1.880.16011420.14093213X-RAY DIFFRACTION100
1.88-2.020.17371460.13643210X-RAY DIFFRACTION100
2.02-2.220.1331460.1513219X-RAY DIFFRACTION100
2.22-2.550.17871440.15323233X-RAY DIFFRACTION100
2.55-3.210.18891460.16773275X-RAY DIFFRACTION100
3.21-28.720.18921530.15543422X-RAY DIFFRACTION100

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