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Yorodumi- PDB-7ju9: Solution NMR structure of Prochlorosin 2.11 (Pcn2.11) produced by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ju9 | ||||||||||||
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Title | Solution NMR structure of Prochlorosin 2.11 (Pcn2.11) produced by Prochlorococcus MIT 9313 | ||||||||||||
Components | Prochlorosin 2.11 | ||||||||||||
Keywords | UNKNOWN FUNCTION / lanthipeptide / cyclic peptide / posttranslational modification / RiPP | ||||||||||||
Function / homology | Nif11 domain / Nif11-like leader peptide / Nif11 domain / Possible Vesiculovirus phosphoprotein Function and homology information | ||||||||||||
Biological species | Prochlorococcus marinus str. MIT 9313 (bacteria) | ||||||||||||
Method | SOLUTION NMR / simulated annealing | ||||||||||||
Authors | Bobeica, S.C. / van der Donk, W.A. / Zhu, L. | ||||||||||||
Funding support | United States, 1items
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Citation | Journal: Chem Sci / Year: 2020 Title: Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways. Authors: Bobeica, S.C. / Zhu, L. / Acedo, J.Z. / Tang, W. / van der Donk, W.A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria. Authors: Li, B. / Sher, D. / Kelly, L. / Shi, Y. / Huang, K. / Knerr, P.J. / Joewono, I. / Rusch, D. / Chisholm, S.W. / van der Donk, W.A. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2017 Title: Evolutionary radiation of lanthipeptides in marine cyanobacteria. Authors: Cubillos-Ruiz, A. / Berta-Thompson, J.W. / Becker, J.W. / van der Donk, W.A. / Chisholm, S.W. #3: Journal: Biochemistry / Year: 2012 Title: Structural characterization of four prochlorosins: a novel class of lantipeptides produced by planktonic marine cyanobacteria. Authors: Tang, W. / van der Donk, W.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ju9.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ju9.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ju9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ju9_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 7ju9_full_validation.pdf.gz | 563 KB | Display | |
Data in XML | 7ju9_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 7ju9_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/7ju9 ftp://data.pdbj.org/pub/pdb/validation_reports/ju/7ju9 | HTTPS FTP |
-Related structure data
Related structure data | 6ve9C 6vgtC 6vhjC 6vjqC 6vljC 7jvfC 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: 1831.042 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prochlorococcus marinus str. MIT 9313 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7V450*PLUS |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0 Not defined / Ionic strength err: _ / pH: 6 / PH err: 0.1 / Pressure: 1 atm / Pressure err: _ / Temperature err: 0.1
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-NMR measurement
NMR spectrometer | Type: Agilent VNMRS / Manufacturer: Agilent / Model: VNMRS / Field strength: 750 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 3 | ||||||||||||||||||||
NMR representative | Selection criteria: medoid | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |