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- PDB-6dmz: Solution structure of ZmD32 -

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Basic information

Entry
Database: PDB / ID: 6dmz
TitleSolution structure of ZmD32
ComponentsFlower-specific gamma-thionin
KeywordsANTIFUNGAL PROTEIN / antimicrobial peptide / plant defensin
Function / homology
Function and homology information


Defensin, plant / Gamma-thionins family signature. / Gamma-thionin family / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Flower-specific gamma-thionin
Similarity search - Component
Biological speciesZea mays (maize)
MethodSOLUTION NMR / simulated annealing
AuthorsHarvey, P.J. / Craik, D.J.
CitationJournal: Front Microbiol / Year: 2019
Title: Salt-Tolerant Antifungal and Antibacterial Activities of the Corn Defensin ZmD32.
Authors: Kerenga, B.K. / McKenna, J.A. / Harvey, P.J. / Quimbar, P. / Garcia-Ceron, D. / Lay, F.T. / Phan, T.K. / Veneer, P.K. / Vasa, S. / Parisi, K. / Shafee, T.M.A. / van der Weerden, N.L. / ...Authors: Kerenga, B.K. / McKenna, J.A. / Harvey, P.J. / Quimbar, P. / Garcia-Ceron, D. / Lay, F.T. / Phan, T.K. / Veneer, P.K. / Vasa, S. / Parisi, K. / Shafee, T.M.A. / van der Weerden, N.L. / Hulett, M.D. / Craik, D.J. / Anderson, M.A. / Bleackley, M.R.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 9, 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flower-specific gamma-thionin


Theoretical massNumber of molelcules
Total (without water)5,4791
Polymers5,4791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3750 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 Flower-specific gamma-thionin


Mass: 5479.359 Da / Num. of mol.: 1 / Fragment: Knot1 domain residues 18-64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Komagataella pastoris (fungus) / References: UniProt: B6SJE6
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 TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
142isotropic12D 1H-1H TOCSY
162isotropic12D 1H-1H NOESY
152isotropic12D 1H-13C HSQC
172isotropic12D 1H-1H ECOSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM peptide, 90% H2O/10% D2OZmD32_sample90% H2O/10% D2O
solution21 mM peptide, 100% D2OZmD32_D2Osample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMpeptidenatural abundance1
1 mMpeptidenatural abundance2
Sample conditionsIonic strength: not defined Not defined / Label: conditions_1 / pH: 3.5 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.1

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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 A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNMRCCPNchemical shift assignment
TopSpinBruker Biospinprocessing
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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