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- PDB-2lr3: Solution structure of the anti-fungal defensin DEF4 (MTR_8g070770... -

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Basic information

Entry
Database: PDB / ID: 2lr3
TitleSolution structure of the anti-fungal defensin DEF4 (MTR_8g070770) from Medicago truncatula (barrel clover)
ComponentsDefensin
KeywordsANTIFUNGAL PROTEIN / fungal disease / antifungal agent
Function / homology
Function and homology information


defense response to fungus / defense response / killing of cells of another organism
Similarity search - Function
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
Biological speciesMedicago truncatula (barrel medic)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsBuchko, G.W. / Smith, T.J. / Shah, D.M.
CitationJournal: Plos One / Year: 2013
Title: Structural and Functional Studies of a Phosphatidic Acid-Binding Antifungal Plant Defensin MtDef4: Identification of an RGFRRR Motif Governing Fungal Cell Entry.
Authors: Sagaram, U.S. / El-Mounadi, K. / Buchko, G.W. / Berg, H.R. / Kaur, J. / Pandurangi, R.S. / Smith, T.J. / Shah, D.M.
History
DepositionMar 21, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Jun 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
Revision 1.3Nov 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defensin


Theoretical massNumber of molelcules
Total (without water)5,3551
Polymers5,3551
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 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Defensin


Mass: 5355.098 Da / Num. of mol.: 1 / Fragment: UNP residues 30-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Strain: A17 / Gene: MTR_049s0004, MTR_8g070770 / Production host: Pichia pastoris (fungus) / References: UniProt: G7L736
Has protein modificationY
Sequence detailsTHE AUTHORS STATE THAT THE GENOMIC SEQUENCE IS CORRECT, HIS62. DURING PCR GENERATION OF THE ...THE AUTHORS STATE THAT THE GENOMIC SEQUENCE IS CORRECT, HIS62. DURING PCR GENERATION OF THE EXPRESSION CLONE, AN ARG WAS OBTAINED IN THIS POSITION INSTEAD.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The first 29 natural residues in the native sequence were removed.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1322D 1H-1H TOCSY
1432D 1H-1H TOCSY
1522D 1H-1H NOESY
1632D 1H-1H NOESY
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
191deuterium exchange

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 15N] protein, 0.01 mM TRIS, 93% H2O/7% D2O93% H2O/7% D2O
21 mM protein, 0.01 mM TRIS, 93% H2O/7% D2O93% H2O/7% D2O
31 mM [U-99% 15N] protein, 0.01 mM TRIS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-99% 15N]1
0.01 mMTRIS-21
1 mMentity-32
0.01 mMTRIS-42
1 mMentity-5[U-99% 15N]3
0.01 mMTRIS-63
Sample conditionsIonic strength: 0.01 / pH: 4.4 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian VNMRSVarianVNMRS7502

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.115Goddarddata analysis
Sparky3.115Goddardpeak picking
Felix2007Accelrys Software Inc.processing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionedata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS. Oxidation of all the cys residues was confirmed by the C-beta chemical shifts for the CYS residues determined from a natural abundance 1H-13C-HSQC spectrum. Restraints for the disfulfide bonds were introduced on the basis of position in similar sequences.
NMR constraintsNOE constraints total: 389 / NOE intraresidue total count: 120 / NOE long range total count: 87 / NOE medium range total count: 57 / NOE sequential total count: 125 / Hydrogen bond constraints total count: 34 / Protein phi angle constraints total count: 22 / Protein psi angle constraints total count: 22
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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