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Yorodumi- PDB-1ozz: NMR structure of antifungal defensin ARD1 from Archaeoprepona demophon -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ozz | ||||||
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Title | NMR structure of 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ozz.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ozz.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ozz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ozz_validation.pdf.gz | 337.9 KB | Display | wwPDB validaton report |
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Full document | 1ozz_full_validation.pdf.gz | 385.7 KB | Display | |
Data in XML | 1ozz_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1ozz_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/1ozz ftp://data.pdbj.org/pub/pdb/validation_reports/oz/1ozz | HTTPS FTP |
-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: 4809.409 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoprepona demophon (one-spotted prepona) Plasmid: pEM2 / 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 ARD1, 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 |