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

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Basic information

Entry
Database: PDB / ID: 8hjd
TitleSolution structure of cysteine-rich peptide Bidentatide (Achyranthes bidentata peptide) with glycation
ComponentsGly-bidentatide
KeywordsPLANT PROTEIN / Cysteine rich peptides
Function / homologybeta-D-fructopyranose
Function and homology information
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 1.1Nov 20, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gly-bidentatide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6062
Polymers3,4261
Non-polymers1801
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area160 Å2
ΔGint2 kcal/mol
Surface area2420 Å2
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 Gly-bidentatide


Mass: 3425.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Achyranthes bidentata (plant)
#2: Sugar ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
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
121isotropic12D 1H-1H TOCSY
131isotropic12D DQF-COSY
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-15N HSQC
161isotropic12D 1H-13C HSQC-TOCSY
172isotropic12D 1H-1H NOESY
182isotropic12D 1H-1H TOCSY
192isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution14 mg/mL Gly-bidentatide, 10 % v/v [U-2H] D2O, 60 % v/v H2O, 30 % v/v [U-2H] acetonitrile, 0.01 % w/v DSS, 60% H2O/10% D2O/30% ACNsample160% H2O/10% D2O/30% ACN
solution24 mg/mL Gly-bidentatide, 70 % v/v [U-2H] D2O, 30 % v/v [U-2H] acetonitrile, 0.01 % w/v DSS, 70% D2O/30% ACNsample270% D2O/30% ACN
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mg/mLGly-bidentatidenatural abundance1
10 % v/vD2O[U-2H]1
60 % v/vH2Onatural abundance1
30 % v/vacetonitrile[U-2H]1
0.01 % w/vDSSnatural abundance1
4 mg/mLGly-bidentatidenatural 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 spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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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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