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- PDB-6x1k: Solution NMR structure of de novo designed TMB2.3 -

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Basic information

Entry
Database: PDB / ID: 6x1k
TitleSolution NMR structure of de novo designed TMB2.3
ComponentsDe novo designed transmembrane beta-barrel TMB2.3
KeywordsMEMBRANE PROTEIN / de novo design / beta-barrel
Function / homologyPorin - #20 / Porin / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsLiang, B. / Vorobieva, A.A. / Chow, C.M. / Baker, D. / Tamm, L.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM072694 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2021
Title: De novo design of transmembrane beta barrels.
Authors: Vorobieva, A.A. / White, P. / Liang, B. / Horne, J.E. / Bera, A.K. / Chow, C.M. / Gerben, S. / Marx, S. / Kang, A. / Stiving, A.Q. / Harvey, S.R. / Marx, D.C. / Khan, G.N. / Fleming, K.G. / ...Authors: Vorobieva, A.A. / White, P. / Liang, B. / Horne, J.E. / Bera, A.K. / Chow, C.M. / Gerben, S. / Marx, S. / Kang, A. / Stiving, A.Q. / Harvey, S.R. / Marx, D.C. / Khan, G.N. / Fleming, K.G. / Wysocki, V.H. / Brockwell, D.J. / Tamm, L.K. / Radford, S.E. / Baker, D.
History
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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:
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Assembly

Deposited unit
A: De novo designed transmembrane beta-barrel TMB2.3


Theoretical massNumber of molelcules
Total (without water)13,5481
Polymers13,5481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein De novo designed transmembrane beta-barrel TMB2.3


Mass: 13547.988 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
111isotropic12D 1H-15N HSQC
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D HNCO
151isotropic13D HN(CA)CO
171isotropic13D HSQC-NOESY-HSQC
161isotropic13D NOESY-TROSY
181isotropic11H-15N hetNOE
191isotropic11D proton

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Sample preparation

DetailsType: micelle
Contents: 1.8 mM [U-98% 13C; U-98% 15N, U-98% 2H] TMB2.3, 200 mM DPC, 10 mM HEPES, 10 mM MES, 10 mM sodium acetate, 50 mM sodium chloride, 0.05 % w/v sodium azide, 90% H2O/10% D2O
Details: TMB2.3 refolded in DPC and buffer switched to NMR buffer at pH6.3
Label: DCN_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.8 mMTMB2.3[U-98% 13C; U-98% 15N, U-98% 2H]1
200 mMDPCnatural abundance1
10 mMHEPESnatural abundance1
10 mMMESnatural abundance1
10 mMsodium acetatenatural abundance1
50 mMsodium chloridenatural abundance1
0.05 % w/vsodium azidenatural abundance1
Sample conditionsDetails: TMB2.3 refolded in DPC and buffer switched to NMR buffer at pH6.3
Ionic strength: 50 mM / Label: DCN_sample / pH: 6.3 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddard, TD, and Kneller, DGdata analysis
hmsISTS. G. Hyberts, A. G. Milbradt, A. B. Wagner, H. Arthanari, G. Wagner,collection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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