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- PDB-1j5b: Solution structure of a hydrophobic analogue of the winter flound... -

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Basic information

Entry
Database: PDB / ID: 1j5b
TitleSolution structure of a hydrophobic analogue of the winter flounder antifreeze protein
ComponentsAntifreeze protein type 1 analogue
KeywordsANTIFREEZE PROTEIN / alpha helix
Function / homologyAntifreeze protein, type I / ice binding / extracellular space / identical protein binding / Ice-structuring protein A / Ice-structuring protein A
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model type detailsminimized average
AuthorsLiepinsh, E. / Otting, G. / Harding, M.M. / Ward, L.G. / Mackay, J.P. / Haymet, A.D.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Solution structure of a hydrophobic analogue of the winter flounder antifreeze protein.
Authors: Liepinsh, E. / Otting, G. / Harding, M.M. / Ward, L.G. / Mackay, J.P. / Haymet, A.D.
History
DepositionMar 22, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionMar 27, 2002ID: 1K16
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: 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 protein type 1 analogue


Theoretical massNumber of molelcules
Total (without water)3,4671
Polymers3,4671
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 / 50structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Antifreeze protein type 1 analogue


Mass: 3466.874 Da / Num. of mol.: 1 / Mutation: T(2,13,24,35)V, A(7,29)K, A(11,33)E / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN PSEUDOPLEURONECTES AMERICANUS (WINTER FLOUNDER).
References: UniProt: Q7SIC4, UniProt: P04002*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
121DQF-COSY
1312D 1H-1H TOCSY
1412D 1H-1H ROESY
2522D 1H-1H NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM peptide; 90% H2O, 10% D2O90% H2O/10% D2O
22 mM peptide; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 7.0 ambient 283 K
20.1 7.0 ambient 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR2.5Brukerprocessing
DYANA1.5Guentertrefinement
OPAL2.6Lginbuehlrefinement
XEASY2.2Bartelsdata analysis
MOLMOL1Koradidata analysis
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 50 / Conformers submitted total number: 20

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