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- PDB-236l: THE RESPONSE OF T4 LYSOZYME TO LARGE-TO-SMALL SUBSTITUTIONS WITHI... -

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Basic information

Entry
Database: PDB / ID: 236l
TitleTHE RESPONSE OF T4 LYSOZYME TO LARGE-TO-SMALL SUBSTITUTIONS WITHIN THE CORE AND ITS RELATION TO THE HYDROPHOBIC EFFECT
ComponentsT4 LYSOZYME
KeywordsHYDROLASE / O-GLYCOSYL / GLYCOSIDASE / BACTERIOLYTIC ENZYME
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
2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.9 Å
AuthorsXu, J. / Baase, W.A. / Baldwin, E. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 1998
Title: The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect.
Authors: Xu, J. / Baase, W.A. / Baldwin, E. / Matthews, B.W.
#1: Journal: Science / Year: 1992
Title: Response of a Protein Structure to Cavity-Creating Mutations and its Relation to the Hydrophobic Effect
Authors: Eriksson, A.E. / Baase, W.A. / Zhang, X.J. / Heinz, D.W. / Blaber, M. / Baldwin, E.P. / 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
DepositionOct 17, 1997Processing site: BNL
Revision 1.0Mar 18, 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)18,8254
Polymers18,6001
Non-polymers2253
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.710, 60.710, 96.710
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: 18600.309 Da / Num. of mol.: 1 / Mutation: C54T, V87A, C97A
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: T4 LYSOZYME GENE / Plasmid: M13 / Cellular location (production host): CYTOPLASM / Gene (production host): T4 LYSOZYME GENE / Production host: Escherichia coli (E. coli) / 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-HED / 2-HYDROXYETHYL DISULFIDE


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


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.8 Å3/Da / Density % sol: 48.3 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
pH: 6.7 / Method: batch method / Details: Remington, S.J., (1978) J. Mol. Biol., 118, 81.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
20.55 M11NaCl
314 mMmercaptoethanol11
41 mM11MgCl2
50.01 Msodium phospahte11
62.2 M11NaH2PO4
71.8 M11K2HPO4

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 12, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 15610 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.039
Reflection
*PLUS
Rmerge(I) obs: 0.032

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Processing

Software
NameClassification
TNTrefinement
UCSDdata reduction
UCSDdata scaling
TNTphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 1.9→10 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.16 --
obs-15610 90 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 116 Å2 / ksol: 0.36 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 10 140 1440
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01213171
X-RAY DIFFRACTIONt_angle_deg1.817672
X-RAY DIFFRACTIONt_dihedral_angle_d14.78020
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008342.5
X-RAY DIFFRACTIONt_gen_planes0.0121895.5
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.0111520
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg14.70
X-RAY DIFFRACTIONt_planar_d0.0082.5
X-RAY DIFFRACTIONt_plane_restr0.0125.5

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