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- PDB-9djp: T4 Lysozyme A73H/G77H/R119H/Q123H co-crystallized with Cu(II)-NTA -

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Basic information

Entry
Database: PDB / ID: 9djp
TitleT4 Lysozyme A73H/G77H/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: 1.17 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)20,25217
Polymers18,7671
Non-polymers1,48416
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.514, 59.514, 96.052
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-488-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18767.498 Da / Num. of mol.: 1 / Mutation: C54T, C97A, A73H, G77H, R119H, Q123H
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 , 7 types, 271 molecules

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


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


Mass: 191.139 Da / Num. of mol.: 3 / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


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


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein: 0.33 mM T4 lysozyme mutant, 2.64 mM Cu(II)-NTA. 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: Mar 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.17→28.42 Å / Num. obs: 66047 / % possible obs: 99.6 % / Redundancy: 10.8 % / Biso Wilson estimate: 10.17 Å2 / CC1/2: 1 / Net I/σ(I): 19.8
Reflection shellResolution: 1.17→1.21 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4603 / CC1/2: 0.878 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→28.42 Å / SU ML: 0.0728 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.9038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1607 2000 3.03 %
Rwork0.1449 63986 -
obs0.1454 65986 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.77 Å2
Refinement stepCycle: LAST / Resolution: 1.17→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 84 255 1642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761449
X-RAY DIFFRACTIONf_angle_d1.11751944
X-RAY DIFFRACTIONf_chiral_restr0.072206
X-RAY DIFFRACTIONf_plane_restr0.0067249
X-RAY DIFFRACTIONf_dihedral_angle_d15.2514562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.20.20871330.17234297X-RAY DIFFRACTION94.92
1.2-1.240.16311420.15864511X-RAY DIFFRACTION100
1.24-1.270.18251430.15324539X-RAY DIFFRACTION100
1.27-1.310.16191430.14284545X-RAY DIFFRACTION99.96
1.31-1.360.17481380.13574520X-RAY DIFFRACTION99.98
1.36-1.420.12881430.1334567X-RAY DIFFRACTION99.96
1.42-1.480.16791440.1254535X-RAY DIFFRACTION100
1.48-1.560.13591420.11914553X-RAY DIFFRACTION100
1.56-1.660.14421460.12324598X-RAY DIFFRACTION99.98
1.66-1.780.15061420.1324563X-RAY DIFFRACTION100
1.78-1.960.14641450.13814601X-RAY DIFFRACTION100
1.96-2.250.16271430.13844629X-RAY DIFFRACTION100
2.25-2.830.16211490.1584680X-RAY DIFFRACTION100
2.83-28.420.16961470.15584848X-RAY DIFFRACTION100

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