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- PDB-2lcn: 1H and 15N assignments of WALP19-P10 peptide in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 2lcn
Title1H and 15N assignments of WALP19-P10 peptide in SDS micelles
ComponentsWALP19-P10 peptide
KeywordsMEMBRANE PROTEIN / Proline distortion / Transmembrane
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsVostrikov, V.V. / Courtney, J.M. / Hinton, J.F. / Koeppe II, R.E.
CitationJournal: To be Published
Title: Comparison of Proline Substitutions at Positions 8 and 10 in WALP19
Authors: Vostrikov, V.V. / Courtney, J.M. / Hinton, J.F. / Koeppe II, R.E.
History
DepositionMay 2, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WALP19-P10 peptide


Theoretical massNumber of molelcules
Total (without water)2,1631
Polymers2,1631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide WALP19-P10 peptide


Mass: 2162.618 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The author states that the sequence is synthetic, there is no natural source.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
2422D 1H-15N HSQC T1
2522D 1H-15N HSQC T2
2622D 1H-15N HSQC NOE
2732D 1H-15N HSQC T1
2832D 1H-15N HSQC T2
2932D 1H-15N HSQC NOE
21022D 1H-15N HSQC T1
21122D 1H-15N HSQC T2
21222D 1H-15N HSQC NOE
21332D 1H-15N HSQC T1
21432D 1H-15N HSQC T2
21532D 1H-15N HSQC NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
17.1 mM WALP19-P10, 465 mM [U-100% 2H] SDS, 3.4 % [U-100% 2H] TFE, 88.3 % H2O, 8.3 % D2O, 32 uM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
23.2 mM [U-100% 15N] amino acids labeled, WALP19-P10, 400 mM [U-100% 2H] SDS, 3.4 % [U-100% 2H] TFE, 88.3 % H2O, 8.3 % D2O, 32 uM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
33.2 mM [U-100% 15N] WALP19-P10, 400 mM [U-100% 2H] SDS, 3.4 % [U-100% 2H] TFE, 88.3 % H2O, 8.3 % D2O, 32 uM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
7.1 mMWALP19-P10-11
465 mMSDS-2[U-100% 2H]1
3.4 %TFE-3[U-100% 2H]1
88.3 %H2O-41
8.3 %D2O-51
32 uMpotassium phosphate-61
3.2 mMWALP19-P10-7[U-100% 15N]2
400 mMSDS-8[U-100% 2H]2
3.4 %TFE-9[U-100% 2H]2
88.3 %H2O-102
8.3 %D2O-112
32 uMpotassium phosphate-122
3.2 mMWALP19-P10-13[U-100% 15N]3
400 mMSDS-14[U-100% 2H]3
3.4 %TFE-15[U-100% 2H]3
88.3 %H2O-163
8.3 %D2O-173
32 uMpotassium phosphate-183
Sample conditions
Conditions-IDpHTemperature (K)
16.0 328 K
26.0 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddarddata analysis
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clorestructure solution
relax1.3.7Edward d'Auvergnemodel-free analysis
PSVS1.3Bhattacharya and Montelionedata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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