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

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Basic information

Entry
Database: PDB / ID: 1qtd
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
2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.5 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 27, 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 / 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: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6702
Polymers18,5161
Non-polymers1541
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.968, 60.968, 97.002
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


Mass: 18516.234 Da / Num. of mol.: 1 / Mutation: C54T, C97A, A129W
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-HED / 2-HYDROXYETHYL DISULFIDE


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: potassium phosphate, sodium phosphate, BME, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: seeding / 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
4oxidized beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Mar 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→32.3 Å / Num. all: 9447 / Num. obs: 8267 / % possible obs: 87.5 % / Redundancy: 3.16 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.0572 / Net I/σ(I): 8.066
Reflection shellResolution: 2.5→2.655 Å / Redundancy: 1.69 % / Rmerge(I) obs: 0.212 / Num. unique all: 3076 / % possible all: 65.34
Reflection
*PLUS
% possible obs: 93 %
Reflection shell
*PLUS
% possible obs: 65.3 %

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Processing

Software
NameClassification
TNTrefinement
TNTphasing
RefinementResolution: 2.5→20 Å / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.168 --
all-8031 -
obs-7438 92.6 %
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 8 46 1355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.818
X-RAY DIFFRACTIONt_dihedral_angle_d18.859
X-RAY DIFFRACTIONt_gen_planes0.013
X-RAY DIFFRACTIONt_nbd0.038
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.859
X-RAY DIFFRACTIONt_plane_restr0.013

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