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- PDB-2l0n: DsbB3 peptide structure in 70% TFE -

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Basic information

Entry
Database: PDB / ID: 2l0n
TitleDsbB3 peptide structure in 70% TFE
ComponentsOxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I
KeywordsMEMBRANE PROTEIN / DsbB / organic solvent / folding
Function / homology:
Function and homology information
Biological speciesEscherichia coli BW2952 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHwang, S. / Hilty, C.
CitationJournal: Proteins / Year: 2011
Title: Folding determinants of disulfide bond forming protein B explored by solution nuclear magnetic resonance spectroscopy.
Authors: Hwang, S. / Hilty, C.
History
DepositionJul 8, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I


Theoretical massNumber of molelcules
Total (without water)3,6961
Polymers3,6961
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I


Mass: 3696.453 Da / Num. of mol.: 1 / Fragment: UNP Residues 70-95 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Escherichia coli BW2952 (bacteria) / References: UniProt: C4ZTM6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H COSY
1312D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1 mM [U-100% 2H] TFE, 1mM DsbB protein fragment, trifluoroethanol/water
Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTFE-1[U-100% 2H]1
1 mMDsbB protein fragment-21
Sample conditionsIonic strength: 0 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CYANAKeller and Wuthrichchemical shift assignment
CYANAKeller and Wuthrichdata analysis
CYANAKeller and Wuthrichprocessing
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichprocessing
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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