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- PDB-2jzc: NMR solution structure of ALG13: The sugar donor subunit of a yea... -

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Basic information

Entry
Database: PDB / ID: 2jzc
TitleNMR solution structure of ALG13: The sugar donor subunit of a yeast N-acetylglucosamine transferase. Northeast Structural Genomics Consortium target YG1
ComponentsUDP-N-acetylglucosamine transferase subunit ALG13
KeywordsTRANSFERASE / Rossmann-like fold / Endoplasmic reticulum / Glycosyltransferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase / N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity / UDP-N-acetylglucosamine transferase complex / dolichol-linked oligosaccharide biosynthetic process / cytoplasmic side of Golgi membrane / endoplasmic reticulum / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Glycosyl transferase, family 28, C-terminal / Glycosyltransferase family 28 C-terminal domain / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylglucosamine transferase subunit ALG13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, X. / Weldeghorghis, T. / Zhang, G. / Imepriali, B. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Structure / Year: 2008
Title: Solution structure of Alg13: the sugar donor subunit of a yeast N-acetylglucosamine transferase.
Authors: Wang, X. / Weldeghiorghis, T. / Zhang, G. / Imperiali, B. / Prestegard, J.H.
History
DepositionJan 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: 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_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine transferase subunit ALG13


Theoretical massNumber of molelcules
Total (without water)25,0981
Polymers25,0981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein UDP-N-acetylglucosamine transferase subunit ALG13 / Asparagine-linked glycosylation protein 13


Mass: 25097.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: ALG13, YGL047W / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P53178, N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D HNCA
1413D HN(CO)CA
1513D HN(COCA)CB
1613D HN(CA)CO
1713D HNCO
1823D 1H-15N NOESY
1923D 1H-13C NOESY
11033D 1H-13C NOESY
11142D S3-TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.35 mM [U-13C; U-15N; U-2H] ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.35 mM [U-15N;U-2H; 13C,1H Leu, Val, Ile.D1 methyl] ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
30.35 mM [U-15N;U-2H; 13C,1H Leu, Val, Ile.D1 methyl; 1H-Phe] ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
40.35 mM [U-13C; U-15N; U-2H] ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 3.5 % w/v acrylamide, 3.5 % w/v (3-acrylamidopropyl)-trimethylammonium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMALG13[U-13C; U-15N; U-2H]1
20 mMsodium phosphate1
100 mMsodium chloride1
0.02 %sodium azide1
0.35 mMALG13[U-15N;U-2H; 13C,1H Leu, Val, Ile.D1 methyl]2
20 mMsodium phosphate2
100 mMsodium chloride2
0.35 mMALG13[U-15N;U-2H; 13C,1H Leu, Val, Ile.D1 methyl; 1H-Phe]3
20 mMsodium phosphate3
100 mMsodium chloride3
0.35 mMALG13[U-13C; U-15N; U-2H]4
20 mMsodium phosphate4
100 mMsodium chloride4
0.02 %sodium azide4
3.5 %acrylamide4
3.5 %(3-acrylamidopropyl)-trimethylammonium chloride4
Sample conditionsIonic strength: 0.1 / pH: 6.7 / Pressure: ambient / Temperature: 297 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY6001
Varian UnityVarianUNITY9002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Simulated annealing with the default XPLOR-NIH refinement protocol
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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