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- PDB-1kdf: NORTH-ATLANTIC OCEAN POUT ANTIFREEZE PROTEIN TYPE III ISOFORM HPL... -

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Basic information

Entry
Database: PDB / ID: 1kdf
TitleNORTH-ATLANTIC OCEAN POUT ANTIFREEZE PROTEIN TYPE III ISOFORM HPLC12 MUTANT, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsANTIFREEZE PROTEIN
KeywordsANTIFREEZE PROTEIN / ICE BINDING PROTEIN / THERMAL HYSTERESIS PROTEIN / GLYCOPROTEIN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Antifreeze, type III / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Type-3 ice-structuring protein HPLC 12
Similarity search - Component
Biological speciesMacrozoarces americanus (ocean pout)
MethodSOLUTION NMR / DG_SUB_EMBED, DGSA, REFINE
AuthorsSonnichsen, F.D. / Deluca, C.I. / Davies, P.L. / Sykes, B.D.
Citation
Journal: Structure / Year: 1996
Title: Refined solution structure of type III antifreeze protein: hydrophobic groups may be involved in the energetics of the protein-ice interaction.
Authors: Sonnichsen, F.D. / DeLuca, C.I. / Davies, P.L. / Sykes, B.D.
#1: Journal: Protein Sci. / Year: 1994
Title: Structure-Function Relationship in the Globular Type III Antifreeze Protein: Identification of a Cluster of Surface Residues Required for Binding to Ice
Authors: Chao, H. / Sonnichsen, F.D. / Deluca, C.I. / Sykes, B.D. / Davies, P.L.
#2: Journal: Science / Year: 1993
Title: The Nonhelical Structure of Antifreeze Protein Type III
Authors: Sonnichsen, F.D. / Sykes, B.D. / Chao, H. / Davies, P.L.
History
DepositionJul 8, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_database_status / 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_database_related.content_type / _pdbx_database_related.details / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 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 PROTEIN


Theoretical massNumber of molelcules
Total (without water)7,5261
Polymers7,5261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50AVERAGE
Representative

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Components

#1: Protein ANTIFREEZE PROTEIN / KDEL


Mass: 7525.890 Da / Num. of mol.: 1 / Mutation: INS(M0), P64A, P65A, INS(K66, D67, E68, L69)
Source method: isolated from a genetically manipulated source
Details: TYPE III ISOFORM HPLC 12, QAE-COMPONENT / Source: (gene. exp.) Macrozoarces americanus (ocean pout) / Tissue: BLOOD / Gene: K38 / Variant: HPLC-12 / Plasmid: JM83 / Gene (production host): K38 / Production host: Escherichia coli (E. coli) / References: UniProt: P19614

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQCOSY
121TOCSY
131NOESY
14115N TOCSY HMQC
1513D-(H)CCH-TOCSY HMQC-J
16115N-NOESYHMQC
1713D-15N/13C-NOESYHSQC

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Sample preparation

Sample conditionspH: 7.6 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: DG_SUB_EMBED, DGSA, REFINE / Software ordinal: 1
NMR ensembleConformer selection criteria: AVERAGE / Conformers calculated total number: 50 / Conformers submitted total number: 1

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