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- PDB-1y03: Solution structure of a recombinant type I sculpin antifreeze protein -

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Basic information

Entry
Database: PDB / ID: 1y03
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: This 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 NaOH95% 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: 278 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 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 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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