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- PDB-2ks6: NMR solution structure of ALG13 --- obtained with iterative CS-Ro... -

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Basic information

Entry
Database: PDB / ID: 2ks6
TitleNMR solution structure of ALG13 --- obtained with iterative CS-Rosetta from backbone NMR data.
ComponentsUDP-N-acetylglucosamine transferase subunit ALG13
KeywordsTRANSFERASE / CS-Rosetta / Cyclic N-oxides / Endoplasmic reticulum / Glycosyltransferase
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 / iterative CS-Rosetta
AuthorsLange, O.F. / Wang, X. / Prestegard, J.H. / Baker, D.
CitationJournal: Science / Year: 2010
Title: NMR structure determination for larger proteins using backbone-only data.
Authors: Raman, S. / Lange, O.F. / Rossi, P. / Tyka, M. / Wang, X. / Aramini, J. / Liu, G. / Ramelot, T.A. / Eletsky, A. / Szyperski, T. / Kennedy, M.A. / Prestegard, J. / Montelione, G.T. / Baker, D.
History
DepositionDec 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 1, 2014Group: Refinement description
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)22,5531
Polymers22,5531
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 22552.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ALG13, YGL047W / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / 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
Details: This structure has been determined only from backbone NMR data: chemical shifts, RDCs and HN-HN NOEs. This data is a subset of the data used for related entry 2jzc.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D HN(CA)CB
1323D HN(CO)CA
1423D HN(COCA)CB
1513D 1H-15N NOESY
1633D 1H-15N NOESY
1713D 1H-13C NOESY
1843D 1H-13C NOESY
1952D S3-TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.35 mM [U-15N; U-2H; 13C,1H Leu, Val, Ile.CD1 methyl] UDP-N-acetylglucosamine transferase subunit ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.35 mM [U-13C; U-15N; U-2H] UDP-N-acetylglucosamine transferase subunit ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.35 mM [U-15N; U-2H; 13C,1H Leu, Val, Ile.cd1 labeled; 1H Phe labeled] UDP-N-acetylglucosamine transferase subunit ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
40.35 mM [U-15N; U-2H; 13C,1H Leu, Val, Ile.cd1 labeled; 1H Phe labeled] UDP-N-acetylglucosamine transferase subunit ALG13, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 100% D2O100% D2O
50.35 mM [U-13C; U-15N; U-2H] UDP-N-acetylglucosamine transferase subunit 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 mMUDP-N-acetylglucosamine transferase subunit ALG13[U-15N; U-2H; 13C,1H Leu, Val, Ile.CD1 methyl]1
20 mMsodium phosphate1
100 mMsodium chloride1
0.02 %sodium azide1
0.35 mMUDP-N-acetylglucosamine transferase subunit ALG13[U-13C; U-15N; U-2H]2
20 mMsodium phosphate2
100 mMsodium chloride2
0.02 %sodium azide2
0.35 mMUDP-N-acetylglucosamine transferase subunit ALG13[U-15N; U-2H; 13C,1H Leu, Val, Ile.cd1 labeled; 1H Phe labeled]3
20 mMsodium phosphate3
100 mMsodium chloride3
0.02 %sodium azide3
0.35 mMUDP-N-acetylglucosamine transferase subunit ALG13[U-15N; U-2H; 13C,1H Leu, Val, Ile.cd1 labeled; 1H Phe labeled]4
20 mMsodium phosphate4
100 mMsodium chloride4
0.02 %sodium azide4
0.35 mMUDP-N-acetylglucosamine transferase subunit ALG13[U-13C; U-15N; U-2H]5
20 mMsodium phosphate5
100 mMsodium chloride5
0.02 %sodium azide5
3.5 w/vacrylamide5
3.5 w/v(3-acrylamidopropyl)-trimethylammonium chloride5
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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, F. et al.processing
NMRViewJohnson, B. et al.data analysis
CYANAGuntert, P. et al.data analysis
CS-ROSETTAShen, Y. et al.refinement
RefinementMethod: iterative CS-Rosetta / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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