[English] 日本語
Yorodumi- PDB-1y03: Solution structure of a recombinant type I sculpin antifreeze protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y03 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of a recombinant type I sculpin antifreeze protein | ||||||
Components | Antifreeze peptide SS-3 | ||||||
Keywords | ANTIFREEZE PROTEIN / type I antifreeze protein / sculpin / NMR spectroscopy / solution structure / a-helix | ||||||
Function / homology | Ice-structuring protein SS-3 Function and homology information | ||||||
Biological species | Myoxocephalus scorpius (shorthorn sculpin) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics | ||||||
Authors | Kwan, A.H.Y. / Fairley, K. / Anderberg, P.I. / Liew, C.W. / Harding, M.M. / Mackay, J.P. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Solution structure of a recombinant type I sculpin antifreeze protein Authors: Kwan, A.H.Y. / Fairley, K. / Anderberg, P.I. / Liew, C.W. / Harding, M.M. / Mackay, J.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1y03.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1y03.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 1y03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y03_validation.pdf.gz | 338.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1y03_full_validation.pdf.gz | 428.6 KB | Display | |
Data in XML | 1y03_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1y03_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/1y03 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/1y03 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 3087.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myoxocephalus scorpius (shorthorn sculpin) Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04367 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||||||||||||||
NMR details | Text: This structure was determined using standard triple-resonance NMR spectroscopy. |
-Sample preparation
Details |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Sample conditions | Ionic strength: low / pH: 5 / Pressure: ambient / Temperature: 278 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
---|---|
Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing, molecular dynamics, torsion angle dynamics Software ordinal: 1 Details: Structure calculations were performed using the package ARIA 1.2. Final stuctures are based on 437 unambiguous restraints, 18 sets of ambiguous restraints, 46 dihedral angle restraints and ...Details: Structure calculations were performed using the package ARIA 1.2. Final stuctures are based on 437 unambiguous restraints, 18 sets of ambiguous restraints, 46 dihedral angle restraints and 18 HN residual dipolar coupling restraints. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 500 / Conformers submitted total number: 20 |