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- PDB-2lcb: Solution Structure of a Minor and Transiently Formed State of a T... -

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Basic information

Entry
Database: PDB / ID: 2lcb
TitleSolution Structure of a Minor and Transiently Formed State of a T4 Lysozyme Mutant
ComponentsLysozyme
KeywordsHYDROLASE / Excited State
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)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailslowest energy, model 1
AuthorsBouvignies, G. / Vallurupalli, P. / Hansen, D. / Correia, B. / Lange, O. / Bah, A. / Vernon, R.M. / Dahlquist, F.W. / Baker, D. / Kay, L.E.
CitationJournal: Nature / Year: 2011
Title: Solution structure of a minor and transiently formed state of a T4 lysozyme mutant.
Authors: Bouvignies, G. / Vallurupalli, P. / Hansen, D.F. / Correia, B.E. / Lange, O. / Bah, A. / Vernon, R.M. / Dahlquist, F.W. / Baker, D. / Kay, L.E.
History
DepositionApr 26, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,5861
Polymers18,5861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 9600Two Step Selection Criteria based on chemical shift score and Rosetta energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lysozyme / Endolysin / Lysis protein / Muramidase


Mass: 18586.283 Da / Num. of mol.: 1 / Mutation: C54T, C97A, L99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: T4 Lysozyme L99A Excited State Structure
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N CT TROSY CPMG
12115N CT TROSY CPMG
1311H CT CPMG
1411H CT CPMG
1511H ZQ/DQ CPMG
1611H ZQ/DQ CPMG
17213C' CT CPMG
18213C' CT CPMG
19313Ca CT CPMG
110313Ca CT CPMG
11141Ha CT CPMG
11241Ha CT CPMG
1134Gly 13Ca CT CPMG
1144Gly 1Ha CT CPMG
1154Gly 1Ha CT CPMG
11611H-15N ZZ exchange
11751H-13C Met ZZ exchange
11812D 1H-15N HSQC
11912D 1H-15N HSQC
12012D 1H-15N HMQC
12112D 1H-15N HMQC
12213D HNCO
12313D HNCO
12423D MQ HNCO
12523D MQ HNCO
12632D 1H-13C HSQC
12732D 1H-13C HSQC
12842D 1H-13C HSQC
12942D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-15N; U-2H] T4 L99A, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM [U-13C; U-15N; U-2H] T4 L99A, 90% H2O/10% D2O90% H2O/10% D2O
31.5 mM [U-13Ca; U-15N] T4 L99A, 100% D2O100% D2O
41.5 mM [U-13C; U-15N; U-50% 2H] T4 L99A, 100% D2O100% D2O
51.5 mM [ U-15N] 13CH3 Met T4 L99A, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMT4 L99A-1[U-15N; U-2H]1
1.5 mMT4 L99A-2[U-13C; U-15N; U-2H]2
1.5 mMT4 L99A-3[U-13Ca; U-15N]3
1.5 mMT4 L99A-4[U-13C; U-15N; U-50% 2H]4
1.5 mMT4 L99A-5[ U-15N] 13CH3 Met5
Sample conditionsIonic strength: 85 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FuDAFlemming Hansenextract peak intensities
CATIAFlemming Hansencpmg data analysis
CS-ROSETTAYang Shen, Robert Vernon, David Baker and Ad Baxstructure solution
CS-ROSETTAYang Shen, Robert Vernon, David Baker and Ad Baxrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1 / Details: CS-Rosetta Loop Building
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Two Step Selection Criteria based on chemical shift score and Rosetta energy
Conformers calculated total number: 9600 / Conformers submitted total number: 10

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