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- PDB-1ssy: Crystal structure of phage T4 lysozyme mutant G28A/I29A/G30A/C54T/C97A -

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Basic information

Entry
Database: PDB / ID: 1ssy
TitleCrystal structure of phage T4 lysozyme mutant G28A/I29A/G30A/C54T/C97A
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
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.
History
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 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Oct 27, 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 1.5Feb 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
B: Lysozyme


Theoretical massNumber of molelcules
Total (without water)37,2292
Polymers37,2292
Non-polymers00
Water1,29772
1
A: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,6141
Polymers18,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,6141
Polymers18,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.020, 53.720, 60.490
Angle α, β, γ (deg.)90.00, 102.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 18614.334 Da / Num. of mol.: 2 / Mutation: G28A/I29A/G30A/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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.1 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 13604 / Biso Wilson estimate: 30.9 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.19refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→18.52 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0.009 / SU B: 7.529 / SU ML: 0.175 / Data cutoff high absF: 1297158.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.523 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 663 4.9 %RANDOM
Rwork0.175 ---
obs0.175 13604 89.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9046 Å2 / ksol: 0.34993 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.06 Å20 Å22.3 Å2
2---1.83 Å20 Å2
3----7.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→18.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 0 72 2688
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
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_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.351.5
X-RAY DIFFRACTIONc_mcangle_it3.522
X-RAY DIFFRACTIONc_scbond_it4.522
X-RAY DIFFRACTIONc_scangle_it6.662.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 103 4.6 %
Rwork0.231 2130 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4BME.PARAMBME.TOP

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