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- PDB-2mz0: Solution NMR Structure of PDFL2.1 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 2mz0
TitleSolution NMR Structure of PDFL2.1 from Arabidopsis thaliana
ComponentsDefensin-like protein 32
KeywordsANTIMICROBIAL PROTEIN / CSAlphaBeta motif / defensin
Function / homologyKnottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / defense response to fungus / killing of cells of another organism / 2-Layer Sandwich / extracellular region / Alpha Beta / Defensin-like protein 32
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsOmidvar, R. / Bohlmann, H. / Xia, Y. / Veglia, G.
CitationJournal: To be Published
Title: Solution NMR Structure of PDFL2.1 from Arabidopsis thaliana
Authors: Omidvar, R. / Bohlmann, H. / Xia, Y. / Veglia, G.
History
DepositionFeb 5, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
Revision 1.2Nov 6, 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: Defensin-like protein 32


Theoretical massNumber of molelcules
Total (without water)6,1521
Polymers6,1521
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 #1lowest energy

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Components

#1: Protein Defensin-like protein 32


Mass: 6152.233 Da / Num. of mol.: 1 / Fragment: UNP residues 27-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g35537, F15O4 / Plasmid: pETtrx_1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q2V4I8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D (H)CCH-TOCSY
1613D H(CCO)NH
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D HNHA

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] protein, 0.04 mM potassium chloride, 0.02 mM potassium phosphate, 1 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-13C; U-15N]1
0.04 mMpotassium chloride-21
0.02 mMpotassium phosphate-31
1 mMsodium azide-41
Sample conditionsIonic strength: 0.16 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.37Schwieters, C. et al.structure solution
NMRPipe7.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardpeak picking
Sparky3.113Goddardchemical shift assignment
TALOS3.80F1Cornilescu, Delaglio and Baxgeometry optimization
TopSpin3.1Bruker Biospincollection
X-PLOR NIH2.37Schwieters, C. et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1431 / NOE intraresidue total count: 183 / NOE long range total count: 404 / NOE medium range total count: 331 / NOE sequential total count: 513 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 37 / Protein psi angle constraints total count: 37
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.66 Å
NMR ensemble rmsDistance rms dev: 0.04 Å

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