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- PDB-8hjc: Solution structure of cysteine-rich peptide Bidentatide (Achyrant... -

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Basic information

Entry
Database: PDB / ID: 8hjc
TitleSolution structure of cysteine-rich peptide Bidentatide (Achyranthes bidentata peptide)
ComponentsBidentatide
KeywordsPLANT PROTEIN / Cysteine rich peptides
Biological speciesAchyranthes bidentata (plant)
MethodSOLUTION NMR / simulated annealing
AuthorsFeng, Y. / He, M. / Zhang, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Fitoterapia / Year: 2022
Title: Discovery of a cysteine-rich peptide with glycation modification from Achyranthes bidentata Blume.
Authors: He, M. / Feng, Y. / Wang, Y. / Cheng, M. / Zhang, X. / Zhang, L.
History
DepositionNov 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Assembly

Deposited unit
A: Bidentatide


Theoretical massNumber of molelcules
Total (without water)3,4261
Polymers3,4261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Bidentatide


Mass: 3425.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Achyranthes bidentata (plant)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic22D 1H-1H TOCSY
131isotropic22D DQF-COSY
141isotropic22D 1H-13C HSQC
151isotropic22D 1H-15N HSQC
161isotropic21H-13C HSQC-TOCSY
172isotropic12D 1H-1H NOESY
182isotropic22D 1H-1H TOCSY
192isotropic22D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution14 mg/mL Bidentatide, 10 % v/v [U-2H] D2O, 60 % w/v H2O, 30 % v/v [U-2H] acetonitrile, 0.01 % w/v DSS, 60% H2O/10% D2O/30% deuterated ACNsample160% H2O/10% D2O/30% deuterated ACN
solution24 mg/mL Bidentatide, 70 % v/v [U-2H] D2O, 30 % v/v [U-2H] acetonitrile, 0.01 % w/v DSS, 70% D2O/30% deuterated ACNsample270% D2O/30% deuterated ACN
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mg/mLBidentatidenatural abundance1
10 % v/vD2O[U-2H]1
60 % w/vH2Onatural abundance1
30 % v/vacetonitrile[U-2H]1
0.01 % w/vDSSnatural abundance1
4 mg/mLBidentatidenatural abundance2
70 % v/vD2O[U-2H]2
30 % v/vacetonitrile[U-2H]2
0.01 % w/vDSSnatural abundance2
Sample conditionsIonic strength: 0 mM / Label: condition1 / pH: 7 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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