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- PDB-1qt6: E11H Mutant of T4 Lysozyme -

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Basic information

Entry
Database: PDB / ID: 1qt6
TitleE11H Mutant of T4 Lysozyme
ComponentsPROTEIN (T4 LYSOZYME)
KeywordsHYDROLASE
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 speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsKuroki, R. / Weaver, L.H. / Matthews, B.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structural basis of the conversion of T4 lysozyme into a transglycosidase by reengineering the active site.
Authors: Kuroki, R. / Weaver, L.H. / Matthews, B.W.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of Bacteriophage T4 Lysozyme Refined at 1.7 A Resolution
Authors: Weaver, L.H. / Matthews, B.W.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure-based Design of a Lysozyme with Altered Catalytic Activity
Authors: Kuroki, R. / Weaver, L.H. / Matthews, B.W.
History
DepositionJun 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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 1.4Feb 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: PROTEIN (T4 LYSOZYME)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7864
Polymers18,6371
Non-polymers1493
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.08, 61.08, 96.76
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 (T4 LYSOZYME)


Mass: 18637.395 Da / Num. of mol.: 1 / Mutation: E11H, 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 / Plasmid: M13 PHS1403 / Production host: Escherichia coli (E. coli) / 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.: 133 / 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 %
Crystal grow
*PLUS
pH: 6.7 / 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
22.0 Mphosphate1reservoir
30.25 M1reservoirNaCl
4beta-mercaptoethanol1reservoir
51
61
71

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Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→53 Å / Num. all: 40327 / Num. obs: 17643 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.8→2 Å / % possible all: 72
Reflection
*PLUS
Num. measured all: 40327

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Processing

Software
NameClassification
TNTrefinement
TNTphasing
RefinementResolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
all0.165 16175 -
obs0.165 16175 92 %
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 6 133 1449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.6
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
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor all: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_plane_restr0.01

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