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- PDB-1ssw: Crystal structure of phage T4 lysozyme mutant Y24A/Y25A/T26A/I27A... -

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Database: PDB / ID: 1ssw
TitleCrystal structure of phage T4 lysozyme mutant Y24A/Y25A/T26A/I27A/C54T/C97A
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 / killing of cells of another organism / defense response to bacterium / host cell cytoplasm
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
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
AuthorsHe, M.M. / Baase, W.A. / Xiao, H. / Heinz, D.W. / Matthews, B.W.
CitationJournal: Protein Sci. / Year: 2004
Title: Alanine-scanning mutagenesis of the beta-sheet region of phage T4 lysozyme suggests that tertiary context has a dominant effect on beta-sheet formation
Authors: He, M.M. / Wood, Z.A. / Baase, W.A. / Xiao, H. / Matthews, B.W.
DepositionMar 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 11, 2012Group: Version format compliance
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.5Oct 27, 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

Structure visualization

Structure viewerMolecule:

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Deposited unit
A: Lysozyme
hetero molecules

Theoretical massNumber of molelcules
Total (without water)18,4502

  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.841, 60.841, 96.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221


#1: Protein Lysozyme / / Lysis protein / Muramidase / Endolysin

Mass: 18372.062 Da / Num. of mol.: 1 / Mutation: Y24A/Y25A/T26A/I27A/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 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol

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

Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %

Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. obs: 10038 / Biso Wilson estimate: 19.7 Å2


MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→19.92 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.953 / Rfactor Rfree error: 0.01 / SU B: 5.064 / SU ML: 0.122 / Data cutoff high absF: 2189817.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.215 508 4.8 %RANDOM
Rwork0.187 ---
obs0.187 10546 88.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.4758 Å2 / ksol: 0.365657 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å29.22 Å20 Å2
2---1.58 Å20 Å2
3---3.17 Å2
Refine analyze
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.13→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 4 70 1364
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.191.5
X-RAY DIFFRACTIONc_mcangle_it4.332
X-RAY DIFFRACTIONc_scbond_it5.612
X-RAY DIFFRACTIONc_scangle_it7.932.5
LS refinement shellResolution: 2.13→2.26 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 53 4.7 %
Rwork0.298 1081 -
obs--57.9 %
Xplor file
Refine-IDSerial noParam fileTopol file

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