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- PDB-1rkl: NMR structure of yeast oligosaccharyltransferase subunit Ost4p -

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Basic information

Entry
Database: PDB / ID: 1rkl
TitleNMR structure of yeast oligosaccharyltransferase subunit Ost4p
ComponentsDolichyl-diphosphooligosaccharide--protein glycosyltransferase 4 kDa subunit
KeywordsTRANSFERASE / membrane protein
Function / homologyOligosaccaryltransferase / Oligosaccharyltransferase subunit ost4p superfamily / Oligosaccaryltransferase / oligosaccharyltransferase complex / protein N-linked glycosylation / protein-macromolecule adaptor activity / endoplasmic reticulum membrane / mitochondrion / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsZubkov, S. / Lennarz, W.J. / Mohanty, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural basis for the function of a minimembrane protein subunit of yeast oligosaccharyltransferase
Authors: Zubkov, S. / Lennarz, W.J. / Mohanty, S.
History
DepositionNov 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 4 kDa subunit


Theoretical massNumber of molelcules
Total (without water)3,9871
Polymers3,9871
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #14closest to the average

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Components

#1: Protein/peptide Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 4 kDa subunit / Oligosaccharyl transferase 4 kDa subunit / OTASE 4 kDa subunit


Mass: 3986.696 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide occurs naturally in Saccharomyces cerevisiae (yeast).
References: UniProt: Q99380, EC: 2.4.1.119

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
1312D TOCSY
2412D TOCSY
151DQF-COSY
261DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1mM Ost4p / Solvent system: 4:4:1 CDCl3:CD3OD:D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.0 ambient 298 K
27.0 ambient 311 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglioprocessing
NMRView5.0.4Johnsondata analysis
CYANA1.0.6Guntertstructure solution
ARIA1.2Linge, Nilgesrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: 287 NOE restraints, 58 dihedral angle restraints, 24 distance restraints from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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