[English] 日本語
Yorodumi- PDB-1pyv: NMR solution structure of the mitochondrial F1b presequence pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pyv | ||||||
---|---|---|---|---|---|---|---|
Title | NMR solution structure of the mitochondrial F1b presequence peptide from Nicotiana plumbaginifolia | ||||||
Components | ATP synthase beta chain, mitochondrial precursor | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Nicotiana plumbaginifolia (curled-leaved tobacco) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Moberg, P. / Nilsson, S. / Stahl, A. / Eriksson, A.C. / Glaser, E. / Maler, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: NMR solution structure of the mitochondrial F1beta presequence from Nicotiana plumbaginifolia Authors: Moberg, P. / Nilsson, S. / Stahl, A. / Eriksson, A.C. / Glaser, E. / Maler, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pyv.cif.gz | 379 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pyv.ent.gz | 317.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pyv_validation.pdf.gz | 338.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1pyv_full_validation.pdf.gz | 501.4 KB | Display | |
Data in XML | 1pyv_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 1pyv_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/1pyv ftp://data.pdbj.org/pub/pdb/validation_reports/py/1pyv | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 5753.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana plumbaginifolia (curled-leaved tobacco) Gene: ATPB OR ATP2-1 / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(de3) References: UniProt: P17614, H+-transporting two-sector ATPase |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1 mM F1b presequence, 300 mM sodium dodecyl phosphate, 30 ul D2O Solvent system: 30 ul D2O |
---|---|
Sample conditions | Ionic strength: 300 mM SDS / pH: 7 / Pressure: ambient / Temperature: 318 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
|
-Processing
NMR software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: The structure is based on a total of 539 restraints: 518 NOE-derived distance constraints, and 21 phi dihedral angle restraints from J-couplings. | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: combination of lowest energy and restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 24 |