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- PDB-1ky0: METHIONINE CORE MUTANT OF T4 LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1ky0
TitleMETHIONINE CORE MUTANT OF T4 LYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE / hydrolase (o-glycosyl) / T4 lysozyme / methionine core mutant / protein engineering / protein folding
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
2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsGassner, N.C. / Baase, W.A. / Mooers, B.H. / Busam, R.D. / Weaver, L.H. / Lindstrom, J.D. / Quillin, M.L. / Matthews, B.W.
Citation
Journal: BIOPHYS.CHEM. / Year: 2003
Title: Multiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability
Authors: Gassner, N.C. / Baase, W.A. / Mooers, B.H. / Busam, R.D. / Weaver, L.H. / Lindstrom, J.D. / Quillin, M.L. / Matthews, B.W.
#1: Journal: Biochemistry / Year: 1999
Title: Methionine and alanine substitutions show that the formation of wild-type-like structure in the carboxy-terminal domain of T4 lysozyme is a rate-limiting step in folding
Authors: Gassner, N.C. / Baase, W.A. / Lindstrom, J. / Lu, J. / Dahlquist, F.W. / Matthews, B.W.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution
Authors: Weaver, L.H. / Matthews, B.W.
History
DepositionFeb 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6644
Polymers18,4391
Non-polymers2253
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.3, 61.3, 96.5
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein LYSOZYME /


Mass: 18439.238 Da / Num. of mol.: 1 / Mutation: C54T,L84M,L91M,C97A,L99M,F153M
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 / Gene: gene E / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Na2PO4, NaCl, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorDetector: AREA DETECTOR
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. all: 14993 / Num. obs: 14993 / % possible obs: 91 % / Redundancy: 2.486 % / Biso Wilson estimate: 26.944 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 10.37
Reflection shellResolution: 1.743→1.825 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.24 / Num. unique all: 2821 / % possible all: 65.83

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Processing

Software
NameClassification
stratdata collection
autostratdata reduction
TNTrefinement
STRATdata reduction
AUTOSTRATdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→30 Å / Stereochemistry target values: TNT PROTGEO /
RfactorNum. reflection
Rwork0.16 -
all-14993
obs-14993
Refinement stepCycle: LAST / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 10 124 1423

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