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- PDB-5uoi: Solution structure of the de novo mini protein HHH_rd1_0142 -

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Basic information

Entry
Database: PDB / ID: 5uoi
TitleSolution structure of the de novo mini protein HHH_rd1_0142
ComponentsHHH_rd1_0142
KeywordsDE NOVO PROTEIN / de novo design / all-alpha / helix-helix-helix / mini protein
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsHouliston, S. / Rocklin, G.J. / Lemak, A. / Carter, L. / Chidyausiku, T.M. / Baker, D. / Arrowsmith, C.H.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Science / Year: 2017
Title: Global analysis of protein folding using massively parallel design, synthesis, and testing.
Authors: Rocklin, G.J. / Chidyausiku, T.M. / Goreshnik, I. / Ford, A. / Houliston, S. / Lemak, A. / Carter, L. / Ravichandran, R. / Mulligan, V.K. / Chevalier, A. / Arrowsmith, C.H. / Baker, D.
History
DepositionJan 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _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
Revision 1.3May 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: HHH_rd1_0142


Theoretical massNumber of molelcules
Total (without water)5,1911
Polymers5,1911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3830 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide HHH_rd1_0142


Mass: 5190.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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
111isotropic23D 15N NOESY
161isotropic23D 13C NOESY (aromatic and aliphatic)
121isotropic13D HNCA
131isotropic13D HNCO
141isotropic13D CBCA(CO)NH
151isotropic13D HBHA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 150 mM unlabeled sodium chloride, 400 uM [U-13C; U-15N] protein, 50 mM unlabeled sodium phosphate, 95% H2O/5% D2O
Details: 150 mM NaCl phosphate buffer (pH 7.4) / Label: 15N/13C sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 mMsodium chlorideunlabeled1
400 uMprotein[U-13C; U-15N]1
50 mMsodium phosphateunlabeled1
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIBrukerAVANCE II8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
ABACUSLemak and Arrowsmithchemical shift assignment
ABACUSLemak and Arrowsmithpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: short restrained dynamics simluation in explicit solvent
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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