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- PDB-225l: GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-C... -

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Basic information

Entry
Database: PDB / ID: 225l
TitleGENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS
ComponentsT4 LYSOZYME
KeywordsHYDROLASE / O-GLYCOSYL / T4 LYSOZYME / CAVITY MUTANTS / LIGAND BINDING / PROTEIN ENGINEERING / PROTEIN DESIGN
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 / PARA-XYLENE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.9 Å
AuthorsBaldwin, E.P. / Baase, W.A. / Zhang, X.-J. / Feher, V. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions.
Authors: Baldwin, E. / Baase, W.A. / Zhang, X. / Feher, V. / Matthews, B.W.
#1: Journal: Nature / Year: 1992
Title: A Cavity-Containing Mutant of T4 Lysozyme is Stabilized by Buried Benzene
Authors: Eriksson, A.E. / Baase, W.A. / Wozniak, J.A. / Matthews, B.W.
#2: Journal: Methods Enzymol. / Year: 1989
Title: Expression and Nitrogen-15 Labeling of Proteins for Proton and Nitrogen-15 Nuclear Magnetic Resonance
Authors: Muchmore, D.C. / Mcintosh, L.P. / Russell, C.B. / Anderson, D.E. / Dahlquist, F.W.
#3: 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
DepositionJun 25, 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_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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)18,8694
Polymers18,6061
Non-polymers2623
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.100, 61.100, 96.800
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: 18606.359 Da / Num. of mol.: 1 / Mutation: L133G
Source method: isolated from a genetically manipulated source
Details: P-XYLENE LIGANDED / Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Cellular location: CYTOPLASM / Gene: GENE E / Plasmid: PHS1403 / Gene (production host): T4 LYSOZYME / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-PXY / PARA-XYLENE


Mass: 106.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSTRUCTURE OF A HYDROPHOBIC CAVITY T4 LYSOZYME MUTANT COMPLEXED WITH PARA-XYLENE.

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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: 56.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALS GROWN IN HANGING DROPS AT 4 DEGREES C. PROTEIN 10-20 MG/ML IN A BUFFER CONTAINING 0.1M NA2PO4 PH 6.6, 0.55 M NACL WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 1.8-2.2M NA/KPO4 PH ...Details: CRYSTALS GROWN IN HANGING DROPS AT 4 DEGREES C. PROTEIN 10-20 MG/ML IN A BUFFER CONTAINING 0.1M NA2PO4 PH 6.6, 0.55 M NACL WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 1.8-2.2M NA/KPO4 PH 6.3-7.1 WITH OXIDIZED/REDUCED BME. CRYSTALS WERE EXPOSED TO P-XYLENE VAPOR IN A CAPILLARY FOR SEVERAL DAYS AT ROOM TEMPERATURE., pH 7.0, vapor diffusion - hanging drop, temperature 277K
PH range: 6.3-7.1
Crystal grow
*PLUS
Method: batch method / Details: Remington, S.J., (1978). J. Mol. Biol., 118, 81. / pH: 6.7
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: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 28, 1991 / Details: GRAPHITE MONOCHROMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / % possible obs: 83 % / Rmerge(I) obs: 0.038
Reflection shellHighest resolution: 1.9 Å / Mean I/σ(I) obs: 2

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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
Starting model: WILD TYPE T4 LYSOZYME

Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.16 --
all-14606 -
obs-14606 83 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 374 Å2 / ksol: 0.94 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 8 145 1441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg1.83
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008
X-RAY DIFFRACTIONt_gen_planes0.012
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.068
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg0
X-RAY DIFFRACTIONt_planar_d0.008
X-RAY DIFFRACTIONt_plane_restr0.012

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