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- PDB-6gwx: Stabilising and Understanding a Miniprotein by Rational Design. -

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Basic information

Entry
Database: PDB / ID: 6gwx
TitleStabilising and Understanding a Miniprotein by Rational Design.
ComponentsOptimised PPa-TYR
KeywordsSTRUCTURAL PROTEIN / Designed miniprotein CH-pi interactions weak non-covalent interactions in protiens solution structure proline-tyrosine interactions
Biological speciesStreptococcus mutans (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsPorter Goff, K.L. / Williams, C. / Baker, E.G. / Nicol, D. / Samphire, J.L. / Zieleniewski, F.L. / Crump, M.P. / Woolfson, D.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
CitationJournal: Biochemistry / Year: 2019
Title: Stabilizing and Understanding a Miniprotein by Rational Redesign.
Authors: Porter Goff, K.L. / Nicol, D. / Williams, C. / Crump, M.P. / Zieleniewski, F. / Samphire, J.L. / Baker, E.G. / Woolfson, D.N.
History
DepositionJun 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Optimised PPa-TYR


Theoretical massNumber of molelcules
Total (without water)3,7911
Polymers3,7911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area3200 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 250structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Optimised PPa-TYR


Mass: 3791.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus mutans (bacteria)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 100ms NOESY
121isotropic22D 100ms NOESY
131isotropic12D 1H-1H TOCSY
141isotropic22D 1H-1H TOCSY
151isotropic11H-15N HSQC
181isotropic11H-13N HSQC
171isotropic12D 1H-1H 250ms NOESY
161isotropic22D 1H-1H 250ms NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM Optimised PPa-TYR, 8.2 mM Na2HPO4, 1.8 mM KH2PO4, 2.7 mM KCL, 137 mM NaCl, 10 % [U-99% 2H] D2O, 90% H2O/10% D2O
Label: PPa_tyr_opt / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMOptimised PPa-TYRnatural abundance1
8.2 mMNa2HPO4natural abundance1
1.8 mMKH2PO4natural abundance1
2.7 mMKCLnatural abundance1
137 mMNaClnatural abundance1
10 %D2O[U-99% 2H]1
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),
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 III70011.7mm TCI cryoprobe
Varian VNMRSVarianVNMRS60025mm cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4.1CCPNchemical shift assignment
CcpNmr Analysis2.4.1CCPNpeak picking
TopSpin3.5Bruker Biospincollection
VNMR4Variancollection
NMRDraw9.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe9.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 250 / Conformers submitted total number: 20

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