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- PDB-1g06: CRYSTAL STRUCTURE OF T4 LYSOZYME MUTANT V149S -

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Basic information

Entry
Database: PDB / ID: 1g06
TitleCRYSTAL STRUCTURE OF T4 LYSOZYME MUTANT V149S
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / O-Glycosyl / 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
2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsXu, J. / Baase, W.A. / Quillin, M.L. / Matthews, B.W.
CitationJournal: Protein Sci. / Year: 2001
Title: Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme.
Authors: Xu, J. / Baase, W.A. / Quillin, M.L. / Baldwin, E.P. / Matthews, B.W.
History
DepositionOct 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 3, 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 1.5Feb 7, 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: PROTEIN (LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8414
Polymers18,6161
Non-polymers2253
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.840, 60.840, 96.820
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 PROTEIN (LYSOZYME)


Mass: 18616.311 Da / Num. of mol.: 1 / Mutation: C54T; C97A; V149S
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Eriksson, A.E., (1993) J. Mol. Biol., 229, 747. / PH range low: 7.1 / PH range high: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.25 M1reservoirNaCl
32.0 Mphosphate1reservoir
4beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: OTHER / Detector: AREA DETECTOR / Date: Sep 4, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 20069 / Num. obs: 17144 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.1
Reflection shellResolution: 1.84→2.03 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.148 / Num. unique all: 4062 / % possible all: 89.7
Reflection
*PLUS
Rmerge(I) obs: 0.03

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
UCSD-systemdata scaling
TNTphasing
RefinementResolution: 1.85→10 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: TNT / Details: None
RfactorNum. reflection% reflectionSelection details
Rwork0.156 ---
all-17144 --
obs-17144 91 %-
Rfree---No cross-validation data was set.
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1307 0 10 149 1466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2

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