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- PDB-1lpy: Multiple Methionine Substitutions in T4 Lysozyme -

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Basic information

Entry
Database: PDB / ID: 1lpy
TitleMultiple Methionine Substitutions in 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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGassner, N.C. / Baase, W.A. / Mooers, B.H.M. / Busam, R.D. / Weaver, L.H. / Lindstrom, J.D. / Quillin, M.L. / Matthews, B.W.
CitationJournal: 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.
History
DepositionMay 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2002Provider: 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_conn ...database_2 / 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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)19,8634
Polymers19,6541
Non-polymers2093
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.220, 60.220, 93.240
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 LYSOZYME / Lysis protein / Muramidase / Endolysin


Mass: 19654.395 Da / Num. of mol.: 1
Mutation: C54T,L84M,V87M,L91M,C97A,L99M,I100M,V103M,G110R,V111M,L118M,L121M,L133M
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: E / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal grow
*PLUS
Method: vapor diffusion / Details: Eriksson, A.E., (1993) J. Mol. Biol., 229, 747. / PH range low: 7.1 / PH range high: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.25 M1reservoirNaCl
32.0 Mphosphate1reservoir
4beta-mercaptoethanol1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→15 Å / Num. all: 23682 / Num. obs: 23682 / % possible obs: 95 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043 / Net I/σ(I): 7.1
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1878
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 15 Å / % possible obs: 96 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
TNTrefinement
CCP4(SCALA)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native T4 Lysozyme

Resolution: 1.65→15 Å / σ(F): 0 / Stereochemistry target values: TNT
Details: Residues ASN 163 and LEU 164 are missing in the electron density.
RfactorNum. reflection% reflection
all0.209 23682 -
obs-23682 95 %
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 10 107 1431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.6
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 15 Å / Rfactor all: 0.209 / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_bond_d / Dev ideal: 0.017

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