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- PDB-257l: AN ADAPTABLE METAL-BINDING SITE ENGINEERED INTO T4 LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 257l
TitleAN ADAPTABLE METAL-BINDING SITE ENGINEERED INTO T4 LYSOZYME
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / METAL 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 / 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: 1.9 Å
AuthorsWray, J.W. / Baase, W.A. / Ostheimer, G.J. / Matthews, B.W.
Citation
Journal: Protein Eng. / Year: 2000
Title: Use of a non-rigid region in T4 lysozyme to design an adaptable metal-binding site.
Authors: Wray, J.W. / Baase, W.A. / Ostheimer, G.J. / Zhang, X.J. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 1992
Title: Structure of a Stabilizing Disulfide Bridge Mutant that Closes the Active-Site Cleft of T4 Lysozyme
Authors: Jacobson, R.H. / Matsumura, M. / Faber, H.R. / Matthews, B.W.
#2: Journal: Science / Year: 1989
Title: Control of Enzyme Activity by an Engineered Disulfide Bond
Authors: Matsumura, M. / Matthews, B.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
DepositionJan 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 11, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: 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 1.4Dec 27, 2023Group: 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: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9284
Polymers18,7021
Non-polymers2253
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.930, 60.930, 96.170
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 PROTEIN (LYSOZYME)


Mass: 18702.449 Da / Num. of mol.: 1 / Mutation: T21H,C54T,C97A,T142H
Source method: isolated from a genetically manipulated source
Details: CYS 54 REPLACED BY THR, CYS 97 REPLACED BY ALA, WITH GUANIDINIUM LIGAND
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato
Description: BACTERIOPHAGE T4 (MUTANT GENE DERIVED FROM THE M13 PLASMID BY CLONING THE T4 LYSOZYME GENE)
Cellular location: CYTOPLASM / Gene: GENE E FROM BACTERIOPHAGE T4 / Plasmid: PHS1403 / Gene (production host): T4 LYSOZYME / 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.: 113 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSTRUCTURE OF A T4 LYSOZYME MUTANT WITH AN ENGINEERED METAL BINDING SITE. THIS MUTANT DESIGNATED APO- ...STRUCTURE OF A T4 LYSOZYME MUTANT WITH AN ENGINEERED METAL BINDING SITE. THIS MUTANT DESIGNATED APO-H2 IS THE PROTEIN WHICH CONTAINS THE METAL BINDING SITE, BUT WITH NO METAL LIGANDS. THE METAL LIGANDS ZN, CO, NI WILL BE DESCRIBED AS SEPARATE PDB FILES AND INCLUDED IN THE PAPER "AN ADAPTABLE METAL-BINDING SITE ENGINEERED INTO T4 LYSOZYME."

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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: 2.75 Å3/Da / Density % sol: 55.35 % / Description: STARTING MODEL WAS CYS-FREE WILDTYPE LYSOZYME
Crystal growpH: 7.5
Details: CRYSTALS GROWN IN HANGING DROPS AT 4 DEGREES C. PROTEIN 10-20 MG/ML IN A BUFFER CONTAINING SODIUM PHOSPHATE PH 5.4, 200 MM NACL, WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 1.8-2.0 M ...Details: CRYSTALS GROWN IN HANGING DROPS AT 4 DEGREES C. PROTEIN 10-20 MG/ML IN A BUFFER CONTAINING SODIUM PHOSPHATE PH 5.4, 200 MM NACL, WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 1.8-2.0 M NA/K PHOSPHATE, 200MM NACL, PH 6.5-7.5, AND 5MM OXIDIZED BME 10% V/V ISOPROPANOL,18% W/V PEG 8000, PH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8-2.0 Msodium potassium phosphate1reservoir
25 mMoxidized BME1reservoir
31 mMprotein1drop
4200 mM1dropNaCl
5100 mMphosphate1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jan 24, 1998 / Details: GRAPHITE MONOCHROMATOR
RadiationMonochromator: NI FILTER/GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 15507 / % possible obs: 89 % / Redundancy: 2 % / Rmerge(I) obs: 0.033
Reflection shellHighest resolution: 1.9 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
TNTrefinement
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: STARTING MODEL WAS CYS-FREE WILDTYPE
RfactorNum. reflection% reflection
Rwork0.174 --
all-15507 -
obs-15507 89 %
Solvent computationSolvent model: BABENET SCALING / Bsol: 626 Å2 / ksol: 1 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 10 113 1421
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.015
X-RAY DIFFRACTIONt_gen_planes0.018
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.065
Software
*PLUS
Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / Rfactor all: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_planar_d0.015
X-RAY DIFFRACTIONt_plane_restr0.018

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