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- PDB-256l: BACTERIOPHAGE T4 LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 256l
TitleBACTERIOPHAGE T4 LYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE / LYSOZYME
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.8 Å
AuthorsFaber, H.R. / Matthews, B.W.
CitationJournal: Nature / Year: 1990
Title: A mutant T4 lysozyme displays five different crystal conformations.
Authors: Faber, H.R. / Matthews, B.W.
History
DepositionFeb 24, 1998Processing site: BNL
Revision 1.0May 27, 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6441
Polymers18,6441
Non-polymers00
Water2,378132
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, 97.600
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 / / M6IT


Mass: 18644.430 Da / Num. of mol.: 1 / Mutation: M6I
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 / References: UniProt: P00720, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.82 Å3/Da / Density % sol: 56 %
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 phosphate11
62.2 M11NaH2PO4
71.8 M11K2HPO4

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: FILM / Detector: FILM / Date: 1990
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 13645 / % possible obs: 65 % / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
TNTrefinement
ROSSMANNdata reduction
CAMBRIDGE/ODPROCdata scaling
CCP4(ROTAVATA)data scaling
TNTphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: WT T4LYS

Resolution: 1.8→30 Å
RfactorNum. reflection% reflection
Rwork0.163 --
all-13645 -
obs-13645 65 %
Solvent computationBsol: 375.4 Å2 / ksol: 0.906 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 0 132 1441
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01513291
X-RAY DIFFRACTIONt_angle_deg2.215871.7
X-RAY DIFFRACTIONt_dihedral_angle_d168130
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.013362
X-RAY DIFFRACTIONt_gen_planes0.0171914
X-RAY DIFFRACTIONt_it5.613291
X-RAY DIFFRACTIONt_nbd0.0273510
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg160
X-RAY DIFFRACTIONt_plane_restr0.0174

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