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- PDB-9djl: T4 Lysozyme D127H/V131H co-crystallized with Cu(II)-NTA -

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Basic information

Entry
Database: PDB / ID: 9djl
TitleT4 Lysozyme D127H/V131H 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: 1.18 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)19,36710
Polymers18,6901
Non-polymers6779
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.055, 60.055, 96.032
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: 18690.438 Da / Num. of mol.: 1 / Mutation: C54T, C97A, D127H, V131H
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, 274 molecules

#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.: 1 / Source method: obtained synthetically / Formula: PO4
#5: 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
#6: Chemical ChemComp-NTA / NITRILOTRIACETIC ACID


Mass: 191.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


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


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Protein: 0.33 mM T4 lysozyme mutant, 0.66 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-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.18→28.66 Å / Num. obs: 66327 / % possible obs: 99.5 % / Redundancy: 10.9 % / Biso Wilson estimate: 12.99 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.5
Reflection shellResolution: 1.18→1.21 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4547 / CC1/2: 0.855 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→28.66 Å / SU ML: 0.0913 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.5875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1741 1983 2.99 %
Rwork0.1541 64289 -
obs0.1547 66272 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.54 Å2
Refinement stepCycle: LAST / Resolution: 1.18→28.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 32 265 1594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711411
X-RAY DIFFRACTIONf_angle_d1.10911906
X-RAY DIFFRACTIONf_chiral_restr0.0817205
X-RAY DIFFRACTIONf_plane_restr0.0064246
X-RAY DIFFRACTIONf_dihedral_angle_d13.0006541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.210.1681320.17354283X-RAY DIFFRACTION94.26
1.21-1.240.19791410.15614552X-RAY DIFFRACTION100
1.24-1.280.20291380.15784559X-RAY DIFFRACTION100
1.28-1.320.16671380.15024541X-RAY DIFFRACTION99.96
1.32-1.370.19411450.14774588X-RAY DIFFRACTION100
1.37-1.420.19661440.14344563X-RAY DIFFRACTION100
1.42-1.490.18191460.13874590X-RAY DIFFRACTION100
1.49-1.560.14861400.12434546X-RAY DIFFRACTION100
1.56-1.660.17371430.13934608X-RAY DIFFRACTION100
1.66-1.790.15741450.1384611X-RAY DIFFRACTION100
1.79-1.970.16971410.15564626X-RAY DIFFRACTION100
1.97-2.260.15031390.14994648X-RAY DIFFRACTION99.92
2.26-2.840.19131490.16774695X-RAY DIFFRACTION99.98
2.84-28.660.17581420.16034879X-RAY DIFFRACTION99.82

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