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- PDB-5o1q: LysF1 sh3b domain structure -

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Basic information

Entry
Database: PDB / ID: 5o1q
TitleLysF1 sh3b domain structure
Componentssh3b domain
KeywordsHYDROLASE / endolysin / sh3b
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / peptidase activity / defense response to bacterium / metal ion binding
Similarity search - Function
Bacterial SH3 domain / Bacterial SH3 domain homologues / CHAP domain profile. / CHAP domain / CHAP domain / SH3-like domain, bacterial-type / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily ...Bacterial SH3 domain / Bacterial SH3 domain homologues / CHAP domain profile. / CHAP domain / CHAP domain / SH3-like domain, bacterial-type / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / SH3 Domains / Papain-like cysteine peptidase superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesKayvirus
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBenesik, M. / Novacek, J. / Janda, L. / Dopitova, R. / Pernisova, M. / Melkova, K. / Tisakova, L. / Doskar, J. / Zidek, L. / Hejatko, J. / Pantucek, R.
CitationJournal: Virus Genes / Year: 2018
Title: Role of SH3b binding domain in a natural deletion mutant of Kayvirus endolysin LysF1 with a broad range of lytic activity.
Authors: Benesik, M. / Novacek, J. / Janda, L. / Dopitova, R. / Pernisova, M. / Melkova, K. / Tisakova, L. / Doskar, J. / Zidek, L. / Hejatko, J. / Pantucek, R.
History
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sh3b domain


Theoretical massNumber of molelcules
Total (without water)11,5311
Polymers11,5311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5960 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein sh3b domain


Mass: 11530.995 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kayvirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q6Y7T6*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HN(CA)CO
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCA
161isotropic13D HN(CO)CA
171isotropic13D (H)CCH-TOCSY
181isotropic23D HNH NOESY
191isotropic23D HCH NOESY
1101isotropic23D HCH NOESY
1111isotropic11D H

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Sample preparation

DetailsType: solution
Contents: 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O
Label: sh3b / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMNa-phosphatenone1
0.25 mMsh3b domain[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 20 mM / Label: sh3b / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIBrukerAVANCE II9502

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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