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- PDB-3l64: T4 Lysozyme S44E/WT* -

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Basic information

Entry
Database: PDB / ID: 3l64
TitleT4 Lysozyme S44E/WT*
ComponentsLysozyme
KeywordsHYDROLASE / hydrolase (O-glycosyl) / Antimicrobial / Bacteriolytic enzyme / 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 / Lysozyme domain superfamily / Phage lysozyme / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBlaber, M. / Zhang, X.-J. / Lindstrom, J.D. / Pepiot, S.D. / Baase, W.A. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Determination of alpha-helix propensity within the context of a folded protein. Sites 44 and 131 in bacteriophage T4 lysozyme.
Authors: Blaber, M. / Zhang, X.J. / Lindstrom, J.D. / Pepiot, S.D. / Baase, W.A. / Matthews, B.W.
History
DepositionDec 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8273
Polymers18,6701
Non-polymers1562
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.100, 35.100, 46.800
Angle α, β, γ (deg.)90.00, 102.00, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-222-

HOH

21A-240-

HOH

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Components

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


Mass: 18670.398 Da / Num. of mol.: 1 / Mutation: S44E, C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 10 Ul of protein solution (20 mg/ml) mixed with 10 Ul of well solution, typically 2.0 M-phosphate (pH 6.3 to 7.1), 0.25 M-NaCl and 6 Ul of 2-hydroxyethyl disulfide/ml (i.e. oxidized beta- ...Details: 10 Ul of protein solution (20 mg/ml) mixed with 10 Ul of well solution, typically 2.0 M-phosphate (pH 6.3 to 7.1), 0.25 M-NaCl and 6 Ul of 2-hydroxyethyl disulfide/ml (i.e. oxidized beta-mercaptoethanol). The drop was then equilibrated over 1 ml of well solution using a Limbro plate, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Multiwire Area Detector / Detector: Xuong-Hamlin / Date: 1993
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→22.9 Å / Num. all: 14841 / Num. obs: 13554 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.9→1.97 Å / Num. unique all: 882 / % possible all: 65

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Processing

Software
NameClassification
X-GENdata scaling
TNTrefinement
X-GENdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→6 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT Protgeo.dat
RfactorNum. reflection% reflection
Rwork0.189 --
obs0.189 13058 91 %
all-13058 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 8 73 1392
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.4

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