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- PDB-6e5c: Solution NMR structure of a de novo designed double-stranded beta... -

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Basic information

Entry
Database: PDB / ID: 6e5c
TitleSolution NMR structure of a de novo designed double-stranded beta-helix
ComponentsDe novo beta protein
KeywordsDE NOVO PROTEIN / beta sheet / beta protein / de novo
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsMarcos, E. / Chidyausiku, T.M. / McShan, A. / Evangelidis, T. / Nerli, S. / Sgourakis, N. / Tripsianes, K. / Baker, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
European CommissionFP7-PEOPLE-2011-IOF 298976 Spain
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: De novo design of a non-local beta-sheet protein with high stability and accuracy.
Authors: Marcos, E. / Chidyausiku, T.M. / McShan, A.C. / Evangelidis, T. / Nerli, S. / Carter, L. / Nivon, L.G. / Davis, A. / Oberdorfer, G. / Tripsianes, K. / Sgourakis, N.G. / Baker, D.
History
DepositionJul 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: De novo beta protein


Theoretical massNumber of molelcules
Total (without water)8,9171
Polymers8,9171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5060 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein De novo beta protein


Mass: 8916.916 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
111anisotropic12D 1H-15N HSQC
121anisotropic14D HC(CC-TOCSY(CO))NH
131anisotropic14D 13C,15N edited HMQC-NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 0.81 mM [U-99% 13C; U-99% 15N] 3NIK, 95% H20/5% H2o
Label: 15N_13C_3NIK / Solvent system: 95% H20/5% H2o
SampleConc.: 0.81 mM / Component: 3NIK / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6.7 / Pressure: 1 bar / 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: Cryoprobe

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Processing

NMR software
NameDeveloperClassification
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
4D-CHAINSEvangelidis, et. al.chemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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