+Open data
-Basic information
Entry | Database: PDB / ID: 6dhr | ||||||
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Title | NMR Solution structure of Rivi3 | ||||||
Components | Rivi3 | ||||||
Keywords | PLANT PROTEIN / cyclotide cyclic peptide | ||||||
Function / homology | Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / defense response / Rivi3 Function and homology information | ||||||
Biological species | Rinorea virgata (plant) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Harvey, P.J. / Craik, D.J. | ||||||
Citation | Journal: J. Nat. Prod. / Year: 2018 Title: Discovery and Characterization of Cyclotides from Rinorea Species. Authors: Niyomploy, P. / Chan, L.Y. / Harvey, P.J. / Poth, A.G. / Colgrave, M.L. / 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 | 6dhr.cif.gz | 165 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dhr.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 6dhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dhr_validation.pdf.gz | 504.8 KB | Display | wwPDB validaton report |
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Full document | 6dhr_full_validation.pdf.gz | 577.4 KB | Display | |
Data in XML | 6dhr_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 6dhr_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/6dhr ftp://data.pdbj.org/pub/pdb/validation_reports/dh/6dhr | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3139.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rinorea virgata (plant) / References: UniProt: A0A4V8GZR4*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 2.0 mg/mL NA peptide, 90% H2O/10% D2O / Label: rivi3_sample / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 2.0 mg/mL / Component: peptide / Isotopic labeling: NA |
Sample conditions | Ionic strength: nd Not defined / Label: conditions_1 / pH: 4.1 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | ||||||||||||||||||||
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 |