+Open data
-Basic information
Entry | Database: PDB / ID: 5gvo | ||||||
---|---|---|---|---|---|---|---|
Title | Solution NMR structure of a new lasso peptide sphaericin | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / lasso peptide / antibacterial / Structure from MOLMOL | ||||||
Function / homology | Putative lasso peptide Function and homology information | ||||||
Biological species | Planomonospora sphaerica (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Hemmi, H. / Kodani, S. / Inoue, Y. / Suzuki, M. / Dohra, H. / Suzuki, T. / Ohnishi-Kameyama, M. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Eur.J.Org.Chem. / Year: 2017 Title: Sphaericin, a Lasso Peptide from the Rare Actinomycete Planomonospora sphaerica Authors: Kodani, S. / Inoue, Y. / Suzuki, M. / Dohra, H. / Suzuki, T. / Hemmi, H. / Ohnishi-Kameyama, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5gvo.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5gvo.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 5gvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gvo_validation.pdf.gz | 378.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5gvo_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 5gvo_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 5gvo_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/5gvo ftp://data.pdbj.org/pub/pdb/validation_reports/gv/5gvo | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 2175.509 Da / Num. of mol.: 1 / Fragment: UNP residues 22-39 / Source method: isolated from a natural source / Source: (natural) Planomonospora sphaerica (bacteria) / References: UniProt: A0A171DJY5 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Type: solution / Contents: 10 mg/mL NA-C,H peptide, DMSO / Label: sample / Solvent system: DMSO |
---|---|
Sample | Conc.: 10 mg/mL / Component: peptide / Isotopic labeling: NA-C,H |
Sample conditions | Ionic strength: not detected Not defined / Label: condition / PH units: Not defined / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 2 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 300 / Conformers submitted total number: 15 |