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- PDB-2lgz: Solution structure of STT3P -

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Basic information

Entry
Database: PDB / ID: 2lgz
TitleSolution structure of STT3P
ComponentsDolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3
KeywordsTRANSFERASE / MEMBRANE PROTEIN / CATALYTIC DOMAIN / OLIGOSACCHARYL TRANSFERASE
Function / homology
Function and homology information


oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / post-translational protein modification / endoplasmic reticulum membrane / endoplasmic reticulum / metal ion binding
Similarity search - Function
: / STT3/PglB/AglB core domain / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal
Similarity search - Domain/homology
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 10
AuthorsHuang, C. / Bhaskaran, R. / Mohanty, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Eukaryotic N-Glycosylation Occurs via the Membrane-anchored C-terminal Domain of the Stt3p Subunit of Oligosaccharyltransferase.
Authors: Huang, C. / Bhaskaran, R. / Mohanty, S.
History
DepositionAug 3, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3


Theoretical massNumber of molelcules
Total (without water)31,4131
Polymers31,4131
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)10 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 / Oligosaccharyl transferase subunit STT3


Mass: 31412.994 Da / Num. of mol.: 1 / Fragment: Lumenal domain residues 465-718
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: STT3, YGL022W / Production host: Escherichia coli (E. coli) / References: UniProt: P39007, 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
1113D HBHA(CO)NH
1213D 1H-15N TOCSY
1313D 1H-15N NOESY
1413D (H)CCH-TOCSY
1513D HNHA
1613D H(CCO)NH

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Sample preparation

DetailsContents: 600 uM [U-13C; U-15N; U-2H] protein, 100 mM [U-100% 2H] SDS
Solvent system: [U-100% 2H] SDS
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMentity-1[U-13C; U-15N; U-2H]1
100 mMSDS-2[U-100% 2H]1
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 328 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA9002

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Processing

NMR softwareName: CYANA / Version: 3 / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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