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- PDB-6xwi: Solution NMR structure of the S0_2.126 designed protein -

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Basic information

Entry
Database: PDB / ID: 6xwi
TitleSolution NMR structure of the S0_2.126 designed protein
ComponentsS0_2.126
KeywordsDE NOVO PROTEIN / designed protein
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAbriata, L.A.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation2015/333 Switzerland
European Research Council (ERC)716058 Switzerland
Swiss National Science Foundation310030-163139 Switzerland
CitationJournal: Science / Year: 2020
Title: De novo protein design enables the precise induction of RSV-neutralizing antibodies.
Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. ...Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. / Corthesy, P. / Georgeon, S. / Villard, M. / Richard, C.A. / Descamps, D. / Delgado, T. / Oricchio, E. / Rameix-Welti, M.A. / Mas, V. / Ervin, S. / Eleouet, J.F. / Riffault, S. / Bates, J.T. / Julien, J.P. / Li, Y. / Jardetzky, T. / Krey, T. / Correia, B.E.
History
DepositionJan 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 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: S0_2.126


Theoretical massNumber of molelcules
Total (without water)8,2091
Polymers8,2091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer by SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4760 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80target function
RepresentativeModel #1target function

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Components

#1: Protein S0_2.126


Mass: 8209.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / 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
113isotropic13D HNCO
123isotropic13D HNCA
133isotropic13D CBCA(CO)NH
143isotropic13D HN(CA)CB
153isotropic13D HN(CO)CA
1123isotropic13D HN(CA)CO
1113isotropic12D 1H-15N HSQC
1102isotropic12D 1H-15N HSQC
192isotropic13D 1H-15N NOESY
182isotropic13D 1H-15N TOCSY
172isotropic13D HNHA
1173isotropic13D (H)CCH-TOCSY
163isotropic12D 1H-13C HSQC aliphatic
1141isotropic12D 1H-1H NOESY
1131isotropic12D 1H-1H TOCSY
1164isotropic12D 1H-1H NOESY
1154isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1500 uM protein 3hb_126543, 20 mM sodium phosphate, 90% H2O/10% D2O3hb_126543_unlabeled90% H2O/10% D2O
solution2500 uM [U-99% 15N] protein 3hb_126543, 20 mM sodium phosphate, 90% H2O/10% D2O3hb_126543 15N labeled90% H2O/10% D2O
solution3400 uM [U-99% 13C; U-99% 15N] protein 3hb_126543, 20 mM sodium phosphate, 90% H2O/10% D2O3hb_126543 13C, 15N90% H2O/10% D2O
solution4500 uM protein 3hb_126543, 20 mM sodium phosphate, 100% D2O3hb_126543 unlabeled in D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMprotein 3hb_126543none1
20 mMsodium phosphatenone1
500 uMprotein 3hb_126543[U-99% 15N]2
20 mMsodium phosphatenone2
400 uMprotein 3hb_126543[U-99% 13C; U-99% 15N]3
20 mMsodium phosphatenone3
500 uMprotein 3hb_126543none4
20 mMsodium phosphatenone4
Sample conditionsIonic strength: 20 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
UNIOT. Herrmannstructure calculation
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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