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- PDB-232l: T4 LYSOZYME MUTANT M120K -

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Basic information

Entry
Database: PDB / ID: 232l
TitleT4 LYSOZYME MUTANT M120K
ComponentsT4 LYSOZYME
KeywordsHYDROLASE / O-GLYCOSYL / GLYCOSIDASE
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
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.73 Å
AuthorsLipscomb, L.A. / Drew, D.L. / Gassner, N. / Baase, W.A. / Matthews, B.W.
CitationJournal: Protein Sci. / Year: 1998
Title: Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme.
Authors: Lipscomb, L.A. / Gassner, N.C. / Snow, S.D. / Eldridge, A.M. / Baase, W.A. / Drew, D.L. / Matthews, B.W.
History
DepositionOct 5, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T4 LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7754
Polymers18,6261
Non-polymers1493
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.930, 60.930, 96.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein T4 LYSOZYME


Mass: 18626.348 Da / Num. of mol.: 1 / Mutation: C54T, C97A, M120K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato
Description: MUTANT GENE DERIVED FROM THE M13 PLASMID BY CLONING THE T4 LYSOZYME GENE
Cell line: S2 / Cellular location: CYTOPLASM / Gene: T4 LYSOZYME / Plasmid: M13 / Gene (production host): T4 LYSOZYME / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: M120K WAS AT 32MG/ML IN A BUFFER CONTAINING 0.1M NA2PO4 PH 6.6, 0.55 M NACL. IT WAS DILUTED BY 1/2 WITH A SOLUTION 2.0M IN NA/KPO4 PH 7.1. THIS WAS ALSO THE WELL SOLUTION. HANGING DROP ...Details: M120K WAS AT 32MG/ML IN A BUFFER CONTAINING 0.1M NA2PO4 PH 6.6, 0.55 M NACL. IT WAS DILUTED BY 1/2 WITH A SOLUTION 2.0M IN NA/KPO4 PH 7.1. THIS WAS ALSO THE WELL SOLUTION. HANGING DROP METHODS WERE USED., pH 7.0, vapor diffusion - hanging drop, temperature 277K
PH range: 6.3-7.1
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop
Details: protein solution is mixed in a 1:1 ratio with precipitant solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.1 Msodium phosphate1drop
20.55 M1dropNaCl
30.02 %1dropNaN3
450 mMoxidized beta-mercaptoethanol1reservoirprecipitant
550 mMreduced beta-mercaptoethanol1reservoirprecipitant
61.8-2.0 Msodium/potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 1, 1997 / Details: GRAPHITE MONOCHROMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 14179 / % possible obs: 67 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.9
Reflection shellResolution: 1.8→1.94 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 3.1 / % possible all: 59.4
Reflection shell
*PLUS
% possible obs: 59.4 %

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Processing

Software
NameVersionClassification
TNTrefinement
SDMSDETECTOR SYSTEM (NIELSEN)data reduction
SDMSDETECTOR SYSTEM (NIELSEN)data scaling
TNTphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 1.73→30 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.173 --
all-16798 -
obs-16798 67 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 412.5 Å2 / ksol: 0.941 e/Å3
Refinement stepCycle: LAST / Resolution: 1.73→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 6 110 1409
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01813170.8
X-RAY DIFFRACTIONt_angle_deg2.3917691.3
X-RAY DIFFRACTIONt_dihedral_angle_d21.6568050
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01342
X-RAY DIFFRACTIONt_gen_planes0.0141895
X-RAY DIFFRACTIONt_it5.65913178
X-RAY DIFFRACTIONt_nbd0.03710
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.014 / Weight: 5

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