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- PDB-5wuz: Morintides mO1 -

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Basic information

Entry
Database: PDB / ID: 5wuz
TitleMorintides mO1
ComponentsMorintide mO1
KeywordsUNKNOWN FUNCTION / cysteine rich peptide / disulphide bond / nature product / Moringa oleifera
Function / homology
Function and homology information


chitin binding / defense response to fungus / killing of cells of another organism
Similarity search - Function
Endochitinase-like / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMoringa oleifera (horseradish tree)
MethodSOLUTION NMR / simulated annealing
AuthorsXiao, T. / Tam, J.P.
CitationJournal: To Be Published
Title: Morintides: 8C-Hevein-like peptides without a protein cargo from the drumstick tree Moringa oleifera
Authors: Kini, S.G. / Wong, K.H. / Tan, W.L. / Xiao, T. / Yang, D. / Tam, J.P.
History
DepositionDec 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Morintide mO1


Theoretical massNumber of molelcules
Total (without water)4,5621
Polymers4,5621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3190 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Morintide mO1


Mass: 4561.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Moringa oleifera (horseradish tree) / References: UniProt: A0A1S6EK91*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY

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Sample preparation

DetailsType: solution
Contents: 1 mM Morintide mO1, 55.55 M H2O, 2.92 M [U-100% 2H] D2O, 0.01 % TFA, 0.3 mM sodium chloride, 95% H2O/5% D2O
Label: mO1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMorintide mO1natural abundance1
55.55 MH2Onatural abundance1
2.92 MD2O[U-100% 2H]1
0.01 %TFAnatural abundance1
0.3 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 0.3 mM / Label: condition1 / pH: 3.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.structure calculation
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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