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- PDB-6o0i: NMR ensemble of computationally designed protein XAA -

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Basic information

Entry
Database: PDB / ID: 6o0i
TitleNMR ensemble of computationally designed protein XAA
ComponentsDesign construct XAA
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsWei, K.Y. / Moschidi, D. / Nerli, S. / Sgourakis, N. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01AI143997 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Computational design of closely related proteins that adopt two well-defined but structurally divergent folds.
Authors: Wei, K.Y. / Moschidi, D. / Bick, M.J. / Nerli, S. / McShan, A.C. / Carter, L.P. / Huang, P.S. / Fletcher, D.A. / Sgourakis, N.G. / Boyken, S.E. / Baker, D.
History
DepositionFeb 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 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
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Design construct XAA
B: Design construct XAA
C: Design construct XAA


Theoretical massNumber of molelcules
Total (without water)33,2843
Polymers33,2843
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7610 Å2
ΔGint-77 kcal/mol
Surface area14950 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 5000back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1fewest violations

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Components

#1: Protein Design construct XAA


Mass: 11094.648 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET28 / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic13D CM-CMHM NOESY
131isotropic13D CM-NHN NOESY
141isotropic13D HNHA-CMHM NOESY
152isotropic12D 1H-15N HSQC
162isotropic13D HN(CA)CB
172isotropic13D HNCA
182isotropic13D HNCO

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1440 uM U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val XAA_MAI(LV)proS, 95% H2O/5% D2ONMR buffer 20mM Sodium Phosphate pH 6.2 100mM NaCl, 0.01% NaN3, 1 U Roche protease inhibitor cocktailXAA_MAI(LV)proS95% H2O/5% D2O
solution2500 uM U-[15N, 13C, 2H] XAA_ILVstar, 95% H2O/5% D2ONMR buffer 20mM Sodium Phosphate pH 6.2 100mM NaCl, 0.01% NaN3, 1 U Roche protease inhibitor cocktailXAA_ILVstar95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
440 uMXAA_MAI(LV)proSU-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val1
500 uMXAA_ILVstarU-[15N, 13C, 2H]2
Sample conditionsIonic strength: 100mM NaCl mM / Label: conditions_XAA_MAI(LV)proS / pH: 6.2 / Pressure: 1 atm / Temperature: 310.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz / Details: TCI cryoprobe

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Processing

NMR software
NameDeveloperClassification
RosettaRohl CA, Strauss CE, Misura KM, Baker Drefinement
SparkyGoddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
RosettaRohl CA, Strauss CE, Misura KM, Baker Dstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 5000 / Conformers submitted total number: 10

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