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- PDB-1qtv: T26E APO STRUCTURE OF T4 LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1qtv
TitleT26E APO STRUCTURE 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: 2.3 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 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 1999Provider: 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
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 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)18,8054
Polymers18,6561
Non-polymers1493
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.220, 61.220, 96.320
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: 18656.373 Da / Num. of mol.: 1 / Mutation: T26E, 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.: 25 / 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: 2.79 Å3/Da / Density % sol: 55.95 %
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
22.0 Mphosphate1reservoir
30.25 M1reservoirNaCl
4beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 75 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Mar 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 9715 / Num. obs: 9358 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.2
Reflection shellResolution: 2.3→2.48 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.223 / Num. unique all: 1740 / % possible all: 92
Reflection
*PLUS
Num. measured all: 30082 / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
TNTrefinement
TNTphasing
RefinementResolution: 2.3→19 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
all0.184 10158 -
obs0.184 9350 92 %
Refinement stepCycle: LAST / Resolution: 2.3→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 6 25 1342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_gen_planes0.014
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / σ(F): 0 / Rfactor all: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_plane_restr0.017

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