[English] 日本語
Yorodumi- PDB-5lw8: NMR solution structure of Helicobacter pylori TonB-CTD (residues ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lw8 | ||||||
---|---|---|---|---|---|---|---|
Title | NMR solution structure of Helicobacter pylori TonB-CTD (residues 194-285) | ||||||
Components | Protein TonB | ||||||
Keywords | METAL TRANSPORT / TonB-dependent iron uptake / C-terminal domain / proline rich domain | ||||||
Function / homology | Function and homology information energy transducer activity / siderophore transport / plasma membrane protein complex / transmembrane transport / protein transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Ciragan, A. / Aranko, A.S. / Tascon, I. / Iwai, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Salt-inducible Protein Splicing in cis and trans by Inteins from Extremely Halophilic Archaea as a Novel Protein-Engineering Tool. Authors: Ciragan, A. / Aranko, A.S. / Tascon, I. / Iwai, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5lw8.cif.gz | 549.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5lw8.ent.gz | 471.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/5lw8 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/5lw8 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 10151.667 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Gene: tonB, HP_1341 / Production host: Escherichia coli (E. coli) / References: UniProt: O25899 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR details | Text: 3D 1H-15N NOESY and 3D 1H-13C NOESY spectra were recorded with a mixing time of 90 ms. |
-Sample preparation
Details | Type: solution Contents: 0.5 mM [U-100% 13C; U-100% 15N] TonB CTD, 90% H2O/10% D2O Details: 20 mM sodium phosphate buffer, pH 6.0 / Label: 15N13C / Solvent system: 90% H2O/10% D2O |
---|---|
Sample | Conc.: 0.5 mM / Component: TonB CTD / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 0.02 mM / Label: 0 / pH: 6 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: molecular dynamics / Software ordinal: 6 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |