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- PDB-2n5q: Solution structure of cystein-rich peptide jS1 from Jasminum sambac -

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Basic information

Entry
Database: PDB / ID: 2n5q
TitleSolution structure of cystein-rich peptide jS1 from Jasminum sambac
Componentscysteine-rich peptide jS1
KeywordsUNKNOWN FUNCTION / cystein-rich peptide
Function / homologyJasmintide 1
Function and homology information
Biological speciesJasminum sambac (Arabian jasmine)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsShin, J. / Kumari, G. / Serra, A. / Nguyen, P.Q.T. / Yoon, H. / Tam, J.P.
CitationJournal: To be Published
Title: Identification of a cysteine-rich peptide family with unusual disulfide connectivity from Jasminum sambac
Authors: Shin, J. / Kumari, G. / Serra, A. / Nguyen, P.Q.T. / Yoon, H. / Sze, S. / Tam, J.P.
History
DepositionJul 24, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cysteine-rich peptide jS1


Theoretical massNumber of molelcules
Total (without water)3,1331
Polymers3,1331
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide cysteine-rich peptide jS1


Mass: 3132.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Jasminum sambac (Arabian jasmine) / References: UniProt: A0A0S2KUN2*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1222D 1H-1H TOCSY
1312D DQF-COSY
1412D 1H-1H NOESY
1522D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-1.0 mM jS1-1, 90 % H2O-2, 10 % D2O-3, 20 mM sodium phosphate-4, 50 mM sodium chloride-5, 0.01 %(w/v) sodium azide-6, 90% H2O/10% D2O90% H2O/10% D2O
20.7-1.0 mM jS1-7, 100 % D2O-8, 20 mM sodium phosphate-9, 50 mM sodium chloride-10, 0.01 %(w/v) na sodium azide-11, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mMjS1-10.7-1.01
90 %H2O-21
10 %D2O-31
20 mMsodium phosphate-41
50 mMsodium chloride-51
0.01 %sodium azide-61
mMjS1-70.7-1.02
100 %D2O-82
20 mMsodium phosphate-92
50 mMsodium chloride-102
0.01 %sodium azide-112
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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