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- PDB-2lr3: Solution structure of the anti-fungal defensin DEF4 (MTR_8g070770... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2lr3 | ||||||
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Title | Solution structure of the anti-fungal defensin DEF4 (MTR_8g070770) from Medicago truncatula (barrel clover) | ||||||
![]() | Defensin | ||||||
![]() | ANTIFUNGAL PROTEIN / fungal disease / antifungal agent | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | closest to the average, model 1 | ||||||
![]() | Buchko, G.W. / Smith, T.J. / Shah, D.M. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.4 KB | Display | ![]() |
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PDB format | ![]() | 260.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 524.7 KB | Display | ![]() |
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Full document | ![]() | 713.7 KB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 5355.098 Da / Num. of mol.: 1 / Fragment: UNP residues 30-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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Sequence details | THE 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: The first 29 natural residues in the native sequence were removed. | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample |
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Sample conditions | Ionic strength: 0.01 / pH: 4.4 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: 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 constraints | NOE 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 representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |