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Yorodumi- PDB-2lyf: High resolution NMR solution structure of the theta-defensin RTD-1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lyf | ||||||
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Title | High resolution NMR solution structure of the theta-defensin RTD-1 | ||||||
Components | RTD-1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / theta-defensin / cyclic peptides / cyclic cystine ladder | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Conibear, A.C. / Rosengren, K. / Harvey, P.J. / Craik, D.J. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structural characterization of the cyclic cystine ladder motif of theta-defensins. Authors: Conibear, A.C. / Rosengren, K.J. / Harvey, P.J. / Craik, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lyf.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lyf.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 2lyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/2lyf ftp://data.pdbj.org/pub/pdb/validation_reports/ly/2lyf | 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: 2110.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase peptide synthesis |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Details: Head-to-tail (Arg-Gly) cyclic peptide | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 4.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: Structures were calculated using the scripts from the RECOORD database. | ||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 107 / NOE intraresidue total count: 63 / NOE long range total count: 6 / NOE medium range total count: 4 / NOE sequential total count: 34 / Hydrogen bond constraints total count: 16 / Protein chi angle constraints total count: 6 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 15 / Protein psi angle constraints total count: 15 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1 |