+Open data
-Basic information
Entry | Database: PDB / ID: 5tj1 | ||||||
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Title | Benenodin-1-dC5, state 1 | ||||||
Components | Benenodin-1 | ||||||
Keywords | UNKNOWN FUNCTION / Lasso peptide RiPPs | ||||||
Function / homology | : / Benenodin family lasso peptide Function and homology information | ||||||
Biological species | Asticcacaulis benevestitus DSM 16100 = ATCC BAA-896 (bacteria) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Zong, C. / Link, A.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Lasso Peptide Benenodin-1 Is a Thermally Actuated [1]Rotaxane Switch. Authors: Zong, C. / Wu, M.J. / Qin, J.Z. / Link, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tj1.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tj1.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tj1_validation.pdf.gz | 451.5 KB | Display | wwPDB validaton report |
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Full document | 5tj1_full_validation.pdf.gz | 686.4 KB | Display | |
Data in XML | 5tj1_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 5tj1_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/5tj1 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/5tj1 | HTTPS FTP |
-Related structure data
Related structure data | 6b5wC C: citing same article (ref.) |
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Similar structure data | |
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: 2033.308 Da / Num. of mol.: 1 / Fragment: UNP residues 22-40 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Asticcacaulis benevestitus DSM 16100 = ATCC BAA-896 (bacteria) Gene: ABENE_08090 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: V4RMX4 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Sample state: anisotropic / Type: 2D 1H-1H NOESY |
-Sample preparation
Details | Type: solution Contents: 2.50 mg/mL NA Benenodin-1-dC5, state 1, 90% H2O/10% D2O Label: Benenodin-1-dC5, state 1 / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 2.50 mg/mL / Component: Benenodin-1-dC5, state 1 / Isotopic labeling: NA |
Sample conditions | Ionic strength: 1 mM / Label: Benenodin-1-dC5, state 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 3 | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |