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- PDB-9fdg: Solution structure of a de novo designed 12-stranded transmembran... -

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Basic information

Entry
Database: PDB / ID: 9fdg
TitleSolution structure of a de novo designed 12-stranded transmembrane beta-barrel in LDAO micelles.
ComponentsTMB12sol9_3
KeywordsMEMBRANE PROTEIN / STRUCTURE FROM CYANA 3.98.15
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMuentener, T. / Hiller, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2024
Title: Sculpting conducting nanopore size and shape through de novo protein design.
Authors: Berhanu, S. / Majumder, S. / Muentener, T. / Whitehouse, J. / Berner, C. / Bera, A.K. / Kang, A. / Liang, B. / Khan, N. / Sankaran, B. / Tamm, L.K. / Brockwell, D.J. / Hiller, S. / Radford, ...Authors: Berhanu, S. / Majumder, S. / Muentener, T. / Whitehouse, J. / Berner, C. / Bera, A.K. / Kang, A. / Liang, B. / Khan, N. / Sankaran, B. / Tamm, L.K. / Brockwell, D.J. / Hiller, S. / Radford, S.E. / Baker, D. / Vorobieva, A.A.
History
DepositionMay 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TMB12sol9_3


Theoretical massNumber of molelcules
Total (without water)20,3491
Polymers20,3491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500target function
RepresentativeModel #1target function

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Components

#1: Protein TMB12sol9_3


Mass: 20349.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N TROSY
161isotropic12D 1H-15N TROSY
121isotropic23D HN(CA)CB
131isotropic23D HNCA
141isotropic23D 1H-15N NOESY
152isotropic23D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle1600 uM [U-13C; U-15N; U-2H] TMB12sol9_3, 5 % [U-2H] D2O, 20 mM sodium phosphate, 1 mM EDTA, 15 mM LDAO, 95% H2O/5% D2O15N13C2H95% H2O/5% D2O
micelle2600 uM [U-15N; U-2H; 99% 1HD-Ile,Leu; 99% 1HG-Val; 99% Ala; 99% Met] TMB12sol9_3, 5 % [U-2H] D2O, 20 mM sodium phosphate, 1 mM EDTA, 15 mM LDAO, 95% H2O/5% D2O13C Methyl95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMTMB12sol9_3[U-13C; U-15N; U-2H]1
5 %D2O[U-2H]1
20 mMsodium phosphatenatural abundance1
1 mMEDTAnatural abundance1
15 mMLDAOnatural abundance1
600 uMTMB12sol9_3[U-15N; U-2H; 99% 1HD-Ile,Leu; 99% 1HG-Val; 99% Ala; 99% Met]2
5 %D2O[U-2H]2
20 mMsodium phosphatenatural abundance2
1 mMEDTAnatural abundance2
15 mMLDAOnatural abundance2
Sample conditionsIonic strength: 20 mM / Label: Standard / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE NEOBrukerAVANCE NEO8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis AssignCCPNchemical shift assignment
CcpNmr Analysis AssignCCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20

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