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- PDB-2ly5: Refined solution structure of recombinant brazzein -

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Basic information

Entry
Database: PDB / ID: 2ly5
TitleRefined solution structure of recombinant brazzein
ComponentsDefensin-like protein
KeywordsPLANT PROTEIN / CYS-SAIL / RDC / brazzein
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 / molecular dynamics
AuthorsCornilescu, C.C. / Cornilescu, G. / Tonelli, M. / Markley, J.L. / Assadi-Porter, F.M.
CitationJournal: Proteins / Year: 2013
Title: Temperature-dependent conformational change affecting Tyr11 and sweetness loops of brazzein.
Authors: Cornilescu, C.C. / Cornilescu, G. / Rao, H. / Porter, S.F. / Tonelli, M. / Derider, M.L. / Markley, J.L. / Assadi-Porter, F.M.
History
DepositionSep 12, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,3801
Polymers6,3801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Defensin-like protein / Brazzein


Mass: 6380.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pentadiplandra brazzeana (plant) / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / References: UniProt: P56552

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2222D 1H-15N HSQC
1312D 1H-13C HSQC
2422D 1H-13C HSQC
1513D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM [U-13C; U-15N] protein, 5 mM sodium chloride, 93% H2O/7% D2O93% H2O/7% D2O
21-2 mM [U-13C; U-15N] protein, 5 mM sodium chloride, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-13C; U-15N]1-21
5 mMsodium chloride-21
mMentity-3[U-13C; U-15N]1-22
5 mMsodium chloride-42
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15 5.2 ambient 310 K
25 5.2 ambient 310 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettdata analysis
PIPPGarrettpeak picking
PIPPGarrettchemical shift assignment
VnmrJVariancollection
TALOSCornilescu, Delaglio and Baxbackbone torsion angles
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / 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: 15

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