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- PDB-259l: AN ADAPTABLE METAL-BINDING SITE ENGINEERED INTO T4 LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 259l
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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 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
DepositionFeb 10, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)18,8324
Polymers18,7021
Non-polymers1303
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.140, 62.140, 96.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: Protein PROTEIN (LYSOZYME) / E.C.3.2.1.17


Mass: 18702.449 Da / Num. of mol.: 1 / Mutation: C54T,C97A,T21H,T142H
Source method: isolated from a genetically manipulated source
Details: T4 LYSOZYME MUTANT WITH CYS 54 REPLACED BY THR, CYS 97 REPLACED BY ALA, THR 21 REPLACED BY HIS, THR 142 REPLACED BY HIS
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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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 ...STRUCTURE OF A T4 LYSOZYME MUTANT WITH AN ENGINEERED METAL BINDING SITE. THIS MUTANT DESIGNATED H2CO IS THE PROTEIN WHICH CONTAINS THE METAL BINDING SITE WITH CO +2 BOUND. THE METAL LIGANDS ZN, AND 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: 2.88 Å3/Da / Density % sol: 57.36 % / Description: STARTING MODEL WAS CYS-FREE WILDTYPE LYSOZYME
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2NACL11
3ISOPROPANOL11
4PEG 800011
5HEPES12
6NACL12
7ISOPROPANOL12
8PEG 800012
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1200-300 mM1reservoirNaCl
220 mMHEPES1reservoir
312-16 %PEG80001reservoir
410 %2-propanol1reservoir
52 mMmetal ion1reservoiras the chloride or acetate salt
61 mMprotein1drop
720 mMHEPES1drop
81

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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: Mar 16, 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: 1.92→20 Å / Num. obs: 15465 / % possible obs: 87 % / Redundancy: 3 % / Rmerge(I) obs: 0.031
Reflection shellHighest resolution: 1.92 Å / Rmerge(I) obs: 0.2 / 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: MOLECULAR REPLACEMENT / Resolution: 1.92→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: STARTING MODEL WAS CYS-FREE WILDTYPE
RfactorNum. reflection% reflection
Rwork0.186 --
all-15465 -
obs-15465 87 %
Solvent computationSolvent model: BABENET SCALING / Bsol: 766 Å2 / ksol: 1 e/Å3
Refinement stepCycle: LAST / Resolution: 1.92→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 3 81 1382
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.3
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_planes0.015
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.106
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg0
X-RAY DIFFRACTIONt_plane_restr0.015
X-RAY DIFFRACTIONt_chiral_restr
X-RAY DIFFRACTIONt_planar_d0.008

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