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- PDB-1qth: THE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND S... -

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Basic information

Entry
Database: PDB / ID: 1qth
TitleTHE INTRODUCTION OF STRAIN AND ITS EFFECTS ON THE STRUCTURE AND STABILITY OF T4 LYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE / STRAIN / STABILITY / MUTANT / T4 LYSOZYME
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsLiu, R. / Baase, W.A. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The introduction of strain and its effects on the structure and stability of T4 lysozyme.
Authors: Liu, R. / Baase, W.A. / Matthews, B.W.
History
DepositionJun 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: LYSOZYME
B: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)37,3772
Polymers37,3772
Non-polymers00
Water2,036113
1
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6881
Polymers18,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6881
Polymers18,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.569, 53.569, 101.871
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the noncrystallographic two-fold

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Components

#1: Protein LYSOZYME


Mass: 18688.480 Da / Num. of mol.: 2 / Mutation: C54T, C97A, A98M
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG3.4K, magnesium chloride, Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMmagnesium chloride11
20.1 MHEPES11
330 %(w/v)PEG340011
4oxidized beta-mercaptoethanol11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 29, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→46.4 Å / Num. all: 25769 / Num. obs: 23171 / % possible obs: 89.92 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.048
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.459 / Num. unique all: 3677 / % possible all: 86.4
Reflection
*PLUS
% possible obs: 85 %
Reflection shell
*PLUS
% possible obs: 86.4 %

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Processing

Software
NameClassification
AMoREphasing
TNTrefinement
XDSdata scaling
RefinementResolution: 1.9→20 Å / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.189 --
all-27813 -
obs-23736 85.34 %
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 0 113 2703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.912
X-RAY DIFFRACTIONt_dihedral_angle_d20.526
X-RAY DIFFRACTIONt_gen_planes0.015
X-RAY DIFFRACTIONt_nbd0.04
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.526
X-RAY DIFFRACTIONt_plane_restr0.015

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