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- PDB-254l: LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 254l
TitleLYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE / 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
BETA-MERCAPTOETHANOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsKuroki, R. / Shoichet, B. / Weaver, L.H. / Matthews, B.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: A relationship between protein stability and protein function.
Authors: Shoichet, B.K. / Baase, W.A. / Kuroki, R. / Matthews, B.W.
#1: Journal: Science / Year: 1993
Title: A Covalent Enzyme-Substrate Intermediate with Saccharide Distortion in a Mutant T4 Lysozyme
Authors: Kuroki, R. / Weaver, L.H. / 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
DepositionNov 10, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Other / Category: pdbx_database_status / reflns
Item: _pdbx_database_status.process_site / _reflns.percent_possible_obs
Revision 1.4Nov 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 2.0Nov 23, 2022Group: Atomic model / Data collection / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_PDB_matrix / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: ORTHOGONAL X,Y,Z AXES WERE REALIGNED FROM A*,B,C TO A,B*,C CRYSTALLOGRAPHIC DIRECTIONS
Provider: repository / Type: Remediation
Revision 2.1Mar 15, 2023Group: Advisory / Category: pdbx_database_remark
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7494
Polymers18,6001
Non-polymers1493
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.000, 61.000, 97.200
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


Mass: 18600.352 Da / Num. of mol.: 1 / Mutation: D20S, C54T, 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 / 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-BME / BETA-MERCAPTOETHANOL


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


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal grow
*PLUS
pH: 6.7 / Method: batch method / Details: Weaver, L.H., (1987) J. Mol. Biol., 193, 189.
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

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.707→30 Å / Num. obs: 20044 / Rmerge(I) obs: 0.0383 / Net I/σ(I): 9.63
Reflection
*PLUS

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.9→30 Å
RfactorNum. reflection% reflection
Rwork0.158 --
all-16021 -
obs-16021 90 %
Solvent computationBsol: 625 Å2 / ksol: 1.14 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1307 0 6 158 1471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONt_bond_d0.0181330
X-RAY DIFFRACTIONt_angle_deg2.3491586
X-RAY DIFFRACTIONt_dihedral_angle_d15.1812
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01635
X-RAY DIFFRACTIONt_gen_planes0.015191
X-RAY DIFFRACTIONt_it4.951327
X-RAY DIFFRACTIONt_nbd0.03421
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.1
X-RAY DIFFRACTIONt_planar_d0.016
X-RAY DIFFRACTIONt_plane_restr0.015

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