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- PDB-9djs: T4 Lysozyme A73H/G77H/T115H/R119H co-crystallized with Cu(II)-NTA... -

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Basic information

Entry
Database: PDB / ID: 9djs
TitleT4 Lysozyme A73H/G77H/T115H/R119H co-crystallized with Cu(II)-NTA (room temperature structure)
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 / ISOPROPYL ALCOHOL / NITRILOTRIACETIC ACID / Endolysin
Similarity search - Component
Biological speciesTequatrovirus T4
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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)19,3997
Polymers18,7951
Non-polymers6056
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.721, 60.721, 97.311
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: 18794.523 Da / Num. of mol.: 1 / Mutation: C54T, C97A, A73H, G77H, T115H, R119H
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 , 5 types, 115 molecules

#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: 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
#4: Chemical ChemComp-NTA / NITRILOTRIACETIC ACID


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Protein: 0.33 mM T4 lysozyme mutant, 4.95 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: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Aug 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→27.61 Å / Num. obs: 30207 / % possible obs: 98 % / Redundancy: 4.4 % / Biso Wilson estimate: 18.98 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.81
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.28 / Num. unique obs: 2908 / CC1/2: 0.488 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→27.61 Å / SU ML: 0.1541 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.7737
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 1964 6.62 %
Rwork0.1754 27707 -
obs0.1769 29671 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.01 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 33 109 1447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01521389
X-RAY DIFFRACTIONf_angle_d1.39991871
X-RAY DIFFRACTIONf_chiral_restr0.0886200
X-RAY DIFFRACTIONf_plane_restr0.0095243
X-RAY DIFFRACTIONf_dihedral_angle_d22.1006529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.28351190.28591696X-RAY DIFFRACTION84.3
1.59-1.630.30351340.27861773X-RAY DIFFRACTION88.16
1.63-1.680.24751300.25721837X-RAY DIFFRACTION90.98
1.68-1.730.23951290.24481908X-RAY DIFFRACTION93.87
1.73-1.80.26861380.23171958X-RAY DIFFRACTION96.24
1.8-1.870.21121350.20691972X-RAY DIFFRACTION97.68
1.87-1.950.20361460.18972029X-RAY DIFFRACTION98.77
1.95-2.060.22541350.18242016X-RAY DIFFRACTION99.81
2.06-2.180.18241450.1692050X-RAY DIFFRACTION99.91
2.18-2.350.20561470.16482052X-RAY DIFFRACTION100
2.35-2.590.21181500.1722045X-RAY DIFFRACTION99.91
2.59-2.960.19821490.17822075X-RAY DIFFRACTION100
2.96-3.730.16211500.15552102X-RAY DIFFRACTION100
3.73-27.610.17431570.14922194X-RAY DIFFRACTION99.58

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