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- PDB-5lo2: Engineering protein stability with atomic precision in a monomeri... -

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Basic information

Entry
Database: PDB / ID: 5lo2
TitleEngineering protein stability with atomic precision in a monomeric miniprotein
ComponentsPPaTyr
KeywordsSTRUCTURAL PROTEIN / Designed miniprotein CH-pi interactions weak non-covalent interactions in protiens solution structure proline-tyrosine interactions
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Cross-wall-targeting lipoprotein motif / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal ...Cell surface antigen I/II A repeat / Streptococcal surface antigen repeat / Streptococcus antigen I/II alanine-rich (Ag I/II A) repeat profile. / Glucan-binding protein C/Surface antigen I/II, V-domain / Glucan-binding protein C/Surface antigen I/II, V-domain superfamily / Glucan-binding protein C / Cross-wall-targeting lipoprotein motif / Adhesin isopeptide-forming adherence domain / Cell surface antigen, C-terminal / Antigen I/II, N-terminal / Cell surface antigen C-terminus / Cell surface antigen I/II C2 terminal domain / Adhesin P1 N-terminal domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Cell surface antigen I/II
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodSOLUTION NMR
AuthorsBaker, E.G. / Hudson, K.L. / Williams, C. / Bartlett, G.G. / Heal, J.W. / Sessions, R.B. / Crump, M.P. / Woolfson, D.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
ERASynBioBB/M005615/1 United Kingdom
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Engineering protein stability with atomic precision in a monomeric miniprotein.
Authors: Baker, E.G. / Williams, C. / Hudson, K.L. / Bartlett, G.J. / Heal, J.W. / Porter Goff, K.L. / Sessions, R.B. / Crump, M.P. / Woolfson, D.N.
History
DepositionAug 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 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: PPaTyr


Theoretical massNumber of molelcules
Total (without water)3,8071
Polymers3,8071
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area2980 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein/peptide PPaTyr


Mass: 3807.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus mutans (bacteria) / References: UniProt: P23504*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-15N HSQC
151isotropic12D 1H-13C HSQC
181isotropic22D 1H-1H NOESY
171isotropic22D 1H-1H NOESY
161isotropic22D 1H-1H NOESY
191isotropic22D DQF-COSY

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Sample preparation

DetailsType: solution / Contents: 1 mM NA PPalphaTyr, 90% H2O/10% D2O
Details: 8.2mM Na2HPO4 pH7.4 ionic strength: 1.8mM KH2PO4 137mM NaCl 13.7mM NAOH
Label: unlabelled_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: PPalphaTyr / Isotopic labeling: NA
Sample conditionsDetails: The sample was prepared in phosphate buffered saline and the pH adjusted to pH 7.4 with NaOH, freeze-dried and then reconstituted in the appropriate volume to give peptide (1 mM), Na2HPO4 (8. ...Details: The sample was prepared in phosphate buffered saline and the pH adjusted to pH 7.4 with NaOH, freeze-dried and then reconstituted in the appropriate volume to give peptide (1 mM), Na2HPO4 (8.2 mM), KH2PO4 (1.8 mM), NaCl (137 mM) and KCl (2.7 mM) and NaOH (13.7 mM).
Ionic strength: 0.1698 M / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III7001microcryoprobe-equipped
Bruker AVANCE IIIBrukerAVANCE III9002TCI 5mm z-PFG cryogenic probe

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Processing

SoftwareName: ARIA / Version: 2.3 / Classification: refinement
NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CcpNmr Analysis2.4.1CCPNchemical shift assignment
CcpNmr Analysis2.4.1CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMR ensembleConformers submitted total number: 20

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