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- PDB-1y04: Solution structure of a recombinant type I sculpin antifreeze protein -

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Entry
Database: PDB / ID: 1y04
TitleSolution structure of a recombinant type I sculpin antifreeze protein
ComponentsAntifreeze peptide SS-3
KeywordsANTIFREEZE PROTEIN / type I antifreeze protein / sculpin / NMR spectroscopy / solution structure / a-helix
Function / homologyIce-structuring protein SS-3
Function and homology information
Biological speciesMyoxocephalus scorpius (shorthorn sculpin)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsKwan, A.H.Y. / Fairley, K. / Anderberg, P.I. / Liew, C.W. / Harding, M.M. / Mackay, J.P.
CitationJournal: 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
DepositionNov 14, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antifreeze peptide SS-3


Theoretical massNumber of molelcules
Total (without water)3,0871
Polymers3,0871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Antifreeze peptide SS-3 / rSS3


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
142HNHA
152HNCA
162HN(CA)CB
172CBCA(CO)NH
182HNCO
192HNCA-ECOSY
1102HET-NOE
NMR detailsText: The structure was determined using standard triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM rSS3; pH adjusted to 5.0 using NaOH.95% H2O/5% D2O
21mM rSS3 U-15N,13C; pH adjusted to 5.0 using NaOH95% H2O/5% D2O
Sample conditionsIonic strength: low / pH: 5 / Pressure: ambient / Temperature: 268 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukerprocessing
XEASY1.3.13Bartels et aldata analysis
Sparky3Goddard and Knellerdata analysis
ARIA1.2Linge et alstructure solution
ARIA1.2Linge et alrefinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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