[English] 日本語
![](img/lk-miru.gif)
- PDB-6vlj: Solution NMR of Prochlorosin 2.8 produced by Prochlorococcus MIT 9313 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vlj | ||||||
---|---|---|---|---|---|---|---|
Title | Solution NMR of Prochlorosin 2.8 produced by Prochlorococcus MIT 9313 | ||||||
![]() | Prochlorosin 2.8 | ||||||
![]() | UNKNOWN FUNCTION / lanthipeptide / cyclic peptide / RiPP / posttranslational modification | ||||||
Function / homology | Nif11 domain / Nif11-like leader peptide / Nif11 domain / Possible REJ domain![]() | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Bobeica, S.C. / Acedo, J.Z. / van der Donk, W.A. / Zhu, L. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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: Chem Sci / Year: 2020 Title: Correction: 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. #2: 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. #3: Journal: Nat.Chem.Biol. / Year: 2013 Title: The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry. Authors: Tang, W. / van der Donk, W.A. #4: 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. #5: 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. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 92.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 67.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 570.1 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ve9C ![]() 6vgtC ![]() 6vhjC ![]() 6vjqC ![]() 7ju9C ![]() 7jvfC C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-
Components
#1: Protein/peptide | Mass: 2057.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pRSFDuet-1 Details (production host): N-terminally His-tagged peptide obtained by co-expression with untagged ProcM Production host: ![]() ![]() |
---|---|
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-
Sample preparation
Details |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||
Sample conditions | Ionic strength: 0 Not defined / Ionic strength err: _ / pH: 6.0 / PH err: 0.1 / Pressure: 1 atm / Pressure err: _ / Temperature err: 0.1
|
-NMR measurement
NMR spectrometer | Type: Agilent VNMRS / Manufacturer: Agilent / Model: VNMRS / Field strength: 750 MHz |
---|
-
Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 5 | ||||||||||||||||||||||||
NMR representative | Selection criteria: medoid | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 200 / Conformers submitted total number: 20 |