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- PDB-6d37: Trp-cage tr16b R16Nva : Elimination of pH Dependent Interactions -

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Basic information

Entry
Database: PDB / ID: 6d37
TitleTrp-cage tr16b R16Nva : Elimination of pH Dependent Interactions
ComponentsALA-TYR-ALA-GLN-TRP-LEU-ALA-ASP-DAL-GLY-PRO-ALA-SER-DAL-NVA-PRO-PRO-PRO-SER
KeywordsDE NOVO PROTEIN / MINIPROTEIN / TRP-CAGE / CIRCULAR PERMUTANT / MICROPROTEIN
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsByrne, A. / Andersen, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GM099899 United States
CitationJournal: Biopolymers / Year: 2019
Title: Reversing the typical pH stability profile of the Trp-cage.
Authors: Graham, K.A. / Byrne, A. / Son, R. / Andersen, N.H.
History
DepositionApr 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALA-TYR-ALA-GLN-TRP-LEU-ALA-ASP-DAL-GLY-PRO-ALA-SER-DAL-NVA-PRO-PRO-PRO-SER


Theoretical massNumber of molelcules
Total (without water)1,8931
Polymers1,8931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1630 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide ALA-TYR-ALA-GLN-TRP-LEU-ALA-ASP-DAL-GLY-PRO-ALA-SER-DAL-NVA-PRO-PRO-PRO-SER


Mass: 1893.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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 TOCSY

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Sample preparation

DetailsType: solution / Contents: 1 mM peptide, 90% H2O/10% D2O / Label: sample1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: peptide / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0.019 M / Ionic strength err: 0.001 / Label: conditions1 / pH: 2.5 / PH err: 0.05 / Pressure: ambient atm / Pressure err: 0.1 / Temperature: 280 K / Temperature err: 1

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger A. T. et.al.structure calculation
SparkyGoddard & Knellerchemical shift calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 32

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