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- PDB-3cdv: Contributions of all 20 amino acids at site 96 to the stability a... -

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Basic information

Entry
Database: PDB / ID: 3cdv
TitleContributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme
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 / Antimicrobial / Bacteriolytic enzyme / Glycosidase
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 speciesBacteriophage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 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 27, 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 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 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 1.4Aug 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)18,7864
Polymers18,6361
Non-polymers1493
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.943, 60.943, 97.511
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 / Lysis protein / Muramidase / Endolysin


Mass: 18636.469 Da / Num. of mol.: 1 / Mutation: R96M
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


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.: 83 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growpH: 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, pH 6.70

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5414
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Nov 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: 1.73→22.23 Å / Num. obs: 19870 / % possible obs: 88.4 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07
Reflection shellResolution: 1.73→1.76 Å / % possible all: 72.5

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
SDMSdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L63

1l63


Resolution: 1.73→22.23 Å / Cross valid method: FMUT-FWT ELECTRON DENSITY MAPS / σ(F): 0 / Stereochemistry target values: TNT5G / Details: NATIVE K = 1.3262 OVERALL B = 0.00000
RfactorNum. reflection% reflectionSelection details
Rfree0.2 --NOT APPLICABLE
Rwork0.2 ---
all0.2 22504 --
obs0.2 19870 88 %-
Solvent computationBsol: 609.15 Å2 / ksol: 0.9 e/Å3
Refinement stepCycle: LAST / Resolution: 1.73→22.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 6 83 1425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg1.411
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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