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- PDB-3c7y: Mutant R96A OF T4 lysozyme in wildtype background at 298K -

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Basic information

Entry
Database: PDB / ID: 3c7y
TitleMutant R96A OF T4 lysozyme in wildtype background at 298K
Componentslysozyme
KeywordsHYDROLASE / BACTERIOPHAGE T4 LYSOZYME / VIRAL LYSOZYME / MUTATIONAL ANALYSIS / PROTEIN ENGINEERING / THERMAL STABILITY / PROTEIN STABILITY / PROTEIN ELECTROSTATICS / PROTEIN STRUCTURE / CATION BINDING / CHARGE BURIAL / HYDROGEN BONDING / HELIX DIPOLE / PROTEIN CREVICES / STERIC STRAIN / TEMPERATURE-SENSITIVE MUTANT
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
BETA-MERCAPTOETHANOL / Endolysin
Similarity search - Component
Biological speciesBacteriophage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMooers, B.H.M.
Citation
Journal: Protein Sci. / Year: 2009
Title: Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme.
Authors: Mooers, B.H. / Baase, W.A. / Wray, J.W. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 2009
Title: Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 --> His.
Authors: Mooers, B.H. / Tronrud, D.E. / Matthews, B.W.
History
DepositionFeb 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6903
Polymers18,5761
Non-polymers1142
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.039, 61.039, 97.092
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsmonomer

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Components

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


Mass: 18576.350 Da / Num. of mol.: 1 / Mutation: R96A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage T4 (virus) / Gene: E / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


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


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 2 M NA/K PHOSPHATE PH 6.7 550 mM NACL 50 MM REDUCED BME, 50 MM OXIDIZED BME , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5414 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: May 7, 1998 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 1.85→24 Å / Num. all: 15819 / Num. obs: 14074 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 / Rsym value: 0.08
Reflection shellResolution: 1.85→1.98 Å / % possible all: 83.1

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Processing

Software
NameVersionClassification
SanDeigo Multiwiredata collection
TNTrefinement
sanDeigo Multiwiredata reduction
SanDeigo Multiwiredata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L63

1l63


Resolution: 1.95→24 Å / Cross valid method: Fmut-Fwt electron density maps / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT5g / Details: Native K = 1.2442 Overall B = 0.00000
RfactorNum. reflection% reflectionSelection details
all0.211 15819 --
obs0.211 14074 89 %-
Rfree---not applicable
Solvent computationSolvent model: BABINET / Bsol: 706.951 Å2 / ksol: 0.9 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.53 Å24.53 Å20 Å2
2--4.53 Å20 Å2
3----9.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 5 54 1372
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg1.41

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