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- PDB-9djf: T4 Lysozyme T109H/G113H co-crystallized with Cu(II)-NTA -

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Basic information

Entry
Database: PDB / ID: 9djf
TitleT4 Lysozyme T109H/G113H 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 / Endolysin
Similarity search - Component
Biological speciesTequatrovirus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,41810
Polymers18,7471
Non-polymers6729
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.882, 59.882, 97.391
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: 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

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Non-polymers , 6 types, 261 molecules

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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NTA / NITRILOTRIACETIC ACID


Mass: 191.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein: 0.33 mM T4 lysozyme mutant, 3.3 mM Cu(II)-NTA. Precipitant: 2.0 M NaH2PO4/K2HPO4, pH 7.0, 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: Nov 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.73→28.62 Å / Num. obs: 21841 / % possible obs: 99.7 % / Redundancy: 11 % / Biso Wilson estimate: 19.05 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.8
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1526 / CC1/2: 0.817 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→27.52 Å / SU ML: 0.1739 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.4158
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1941 2002 9.18 %
Rwork0.1592 19797 -
obs0.1624 21799 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.76 Å2
Refinement stepCycle: LAST / Resolution: 1.73→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 35 252 1588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831373
X-RAY DIFFRACTIONf_angle_d1.06151843
X-RAY DIFFRACTIONf_chiral_restr0.0518200
X-RAY DIFFRACTIONf_plane_restr0.006236
X-RAY DIFFRACTIONf_dihedral_angle_d13.6958527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.29251350.21091331X-RAY DIFFRACTION96.32
1.77-1.820.23261450.18581416X-RAY DIFFRACTION100
1.82-1.870.21891350.17261395X-RAY DIFFRACTION100
1.87-1.930.20121380.16991394X-RAY DIFFRACTION100
1.93-20.19741440.16821395X-RAY DIFFRACTION100
2-2.080.18761390.15241402X-RAY DIFFRACTION100
2.08-2.170.17621440.15041393X-RAY DIFFRACTION100
2.17-2.290.17841420.14951411X-RAY DIFFRACTION100
2.29-2.430.18181390.15851407X-RAY DIFFRACTION100
2.43-2.620.2121450.16081414X-RAY DIFFRACTION100
2.62-2.880.22151410.17031433X-RAY DIFFRACTION100
2.88-3.30.20961470.15491429X-RAY DIFFRACTION99.94
3.3-4.150.1831510.14291449X-RAY DIFFRACTION100
4.15-27.520.16841570.16271528X-RAY DIFFRACTION99.88

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