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Yorodumi- PDB-1y04: Solution structure of a recombinant type I sculpin antifreeze protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y04 | ||||||
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y04.cif.gz | 169.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y04.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 1y04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/1y04 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/1y04 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using standard triple-resonance NMR spectroscopy. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: low / pH: 5.0 / Pressure: ambient / Temperature: 268 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
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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 452 unambiguous restraints, 31 sets of ambiguous restraints and 52 dihedral angle 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 |