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Yorodumi- PDB-1p00: NMR structure of ETD151, mutant of the antifungal defensin ARD1 f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p00 | ||||||
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Title | NMR structure of ETD151, mutant of the antifungal defensin ARD1 from Archaeoprepona demophon | ||||||
Components | defensin ARD1 | ||||||
Keywords | ANTIFUNGAL PROTEIN / ALPHA-BETA PROTEIN / CSAB MOTIF (CYSTEINE STABILIZED ALPHA-HELIX BETA-SHEET MOTIF) | ||||||
Function / homology | Function and homology information antifungal humoral response / defense response / killing of cells of another organism / innate immune response / extracellular region Similarity search - Function | ||||||
Biological species | Archaeoprepona demophon (one-spotted prepona) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Landon, C. / Guenneugues, M. / Barbault, F. / Legrain, M. / Menin, L. / Schott, V. / Vovelle, F. / Dimarcq, J.L. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Lead optimization of antifungal peptides with 3D NMR structures analysis. Authors: Landon, C. / Barbault, F. / Legrain, M. / Menin, L. / Guenneugues, M. / Schott, V. / Vovelle, F. / Dimarcq, J.L. | ||||||
History |
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Remark 999 | SEQUENCE AT THE TIME OF PROCESSING, NO SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THIS SEQUENCE. ...SEQUENCE AT THE TIME OF PROCESSING, NO SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THIS SEQUENCE. THERE IS A N19R MUTATION COMPARED TO THE WILD TYPE SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p00.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p00.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 1p00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/1p00 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/1p00 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4852.500 Da / Num. of mol.: 1 / Mutation: N19R Source method: isolated from a genetically manipulated source Details: ETD151 mutant Source: (gene. exp.) Archaeoprepona demophon (one-spotted prepona) Plasmid: pEM51 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P84156 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: homonuclear 2D DQF-COSY, TOCSY, NOESY |
NMR details | Text: determined using standard 2D homonuclear techniques |
-Sample preparation
Details | Contents: 2mM ETD151, 40mM Na acetate buffer / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 40mM Na acetate buffer / pH: 4.3 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy and the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 10 |