+Open data
-Basic information
Entry | Database: PDB / ID: 6b5w | |||||||||
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Title | Benenodin-1-dC5, state 2 | |||||||||
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 | Link, A.J. / Zong, C. | |||||||||
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 | 6b5w.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b5w.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 6b5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b5w_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 6b5w_full_validation.pdf.gz | 667.9 KB | Display | |
Data in XML | 6b5w_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 6b5w_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/6b5w ftp://data.pdbj.org/pub/pdb/validation_reports/b5/6b5w | 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: 2033.308 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Asticcacaulis benevestitus DSM 16100 = ATCC BAA-896 (bacteria) Gene: ABENE_08090 / Plasmid: pCZ35 / 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: 6.15 mg/mL benonedin-1-dC5, state 2, 95% H2O/5% D2O Label: benonedin-1-dC5, state 2 / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 6.15 mg/mL / Component: benonedin-1-dC5, state 2 / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: 1 Not defined / Label: benonedin-1-dC5, state 2 / 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 |