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- PDB-5y22: NMR-Based Model of the 22 Amino Acid Peptide in Polysialyltransfe... -

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Basic information

Entry
Database: PDB / ID: 5y22
TitleNMR-Based Model of the 22 Amino Acid Peptide in Polysialyltransferase Domain (PSTD) of the Polysialyltransferase ST8Sia IV
Components22AA-PSTD peptide
KeywordsSUGAR BINDING PROTEIN / Polysialyltransferase Domain (PSTD) Polysialyltransferase ST8Sia IV Polysialic Acid (Polysia)
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Sialyltransferases / ganglioside biosynthetic process / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / sialyltransferase activity / sialylation / Sialic acid metabolism / sialic acid binding / oligosaccharide metabolic process / N-glycan processing / NCAM1 interactions ...Transferases; Glycosyltransferases; Sialyltransferases / ganglioside biosynthetic process / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / sialyltransferase activity / sialylation / Sialic acid metabolism / sialic acid binding / oligosaccharide metabolic process / N-glycan processing / NCAM1 interactions / protein glycosylation / protein modification process / nervous system development / Golgi membrane / Golgi apparatus / extracellular region
Similarity search - Function
Glycosyl transferase family 29 / Sialyltransferase / GT29-like superfamiliy / Glycosyltransferase family 29 (sialyltransferase)
Similarity search - Domain/homology
CMP-N-acetylneuraminate-poly-alpha-2,8-sialyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLu, B. / Liao, S.M. / Huang, J.M. / Lu, Z.L. / Chen, D. / Liu, X.H. / Zhou, G.P. / Huang, R.B.
Funding support China, 4items
OrganizationGrant numberCountry
National Science Foundation of China31570061 China
National Science Foundation of China31560251 China
National Science Foundation of Guangxi2015GXNSFAA139053 China
Key Research and Development Program of GuangxiAB16380024 China
CitationJournal: To Be Published
Title: NMR-Based Model of the 22 Amino Acid Peptide in Polysialyltransferase Domain (PSTD) of the Polysialyltransferase ST8Sia IV
Authors: Lu, B. / Liao, S.M. / Chen, D. / Liu, X.H. / Zhou, G.P. / Huang, R.B.
History
DepositionJul 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 15, 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: 22AA-PSTD peptide


Theoretical massNumber of molelcules
Total (without water)2,6241
Polymers2,6241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2520 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide 22AA-PSTD peptide


Mass: 2624.181 Da / Num. of mol.: 1 / Fragment: UNP residues 258-279 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92187, EC: 2.4.99.-

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.0 mM 22AA-PSTD peptide, 40 % trifluoroethanol-d3, trifluoroethanol/water
Details: 40%TFE 60% Water / Label: no_polySia / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mM22AA-PSTD peptidenone1
40 %trifluoroethanol-d3none1
Sample conditionsIonic strength: 0 mM / Label: condition1 / pH: 6.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe8.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Analysis2.4CCPNdata analysis
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure calculation
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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