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- PDB-2kyq: 1H, 15N, 13C chemical shifts and structure of CKR-brazzein -

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Basic information

Entry
Database: PDB / ID: 2kyq
Title1H, 15N, 13C chemical shifts and structure of CKR-brazzein
ComponentsDefensin-like protein
KeywordsPLANT PROTEIN / SWEET-TASTING PROTEIN
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Defensin-like protein
Similarity search - Component
Biological speciesPentadiplandra brazzeana (plant)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 9
AuthorsDittli, S.M. / Assadi-Porter, F.M. / Rao, H. / Tonelli, M.
Citation
Journal: Chem Senses / Year: 2011
Title: Structural role of the terminal disulfide bond in the sweetness of brazzein.
Authors: Dittli, S.M. / Rao, H. / Tonelli, M. / Quijada, J. / Markley, J.L. / Max, M. / Assadi-Porter, F.
#1: Journal: To be Published
Title: Insights into the sweetness of brazzein from beta-hairpin peptides derived from the N- and C- termini of brazzein
Authors: Dittli, S.M.
History
DepositionJun 7, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Nov 30, 2011Group: Database references
Revision 1.4Nov 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 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,4081
Polymers6,4081
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Defensin-like protein / Brazzein


Mass: 6408.243 Da / Num. of mol.: 1 / Mutation: K3C, C4K, K5R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pentadiplandra brazzeana (plant) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3) RIPL / References: UniProt: P56552
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Triple brazzein mutant: K3C,C4K,K5R
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D H(CCO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11122D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
1mM [U-99% 13C; U-99% 15N] CKR-brazzein, 17 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
2mM [U-99% 15N] CKR-brazzein, 17 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCKR-brazzein-1[U-99% 13C; U-99% 15N]0.3-11
17 uMDSS-21
mMCKR-brazzein-3[U-99% 15N]0.3-12
17 uMDSS-42
Sample conditionspH: 5.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
PSVSBhattacharya and Montelionevalidation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 741 / NOE intraresidue total count: 157 / NOE long range total count: 213 / NOE medium range total count: 134 / NOE sequential total count: 249 / Hydrogen bond constraints total count: 28 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 94 / Protein psi angle constraints total count: 94
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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