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- PDB-1c8a: NMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 ... -

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Basic information

Entry
Database: PDB / ID: 1c8a
TitleNMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 SA STRUCTURES
ComponentsPROTEIN (ANTIFREEZE PROTEIN TYPE III)
KeywordsANTIFREEZE PROTEIN / ANTIFREEZE / THERMAL HYSTERESIS PROTEIN / ICE BINDING PROTEIN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
SAF domain / SAF / SAF domain / 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
Ice-structuring protein RD3
Similarity search - Component
Biological speciesPachycara brachycephalum (Antarctic eelpout)
MethodSOLUTION NMR / SA
AuthorsMiura, K. / Tsuda, S.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: NMR analysis of type III antifreeze protein intramolecular dimer. Structural basis for enhanced activity.
Authors: Miura, K. / Ohgiya, S. / Hoshino, T. / Nemoto, N. / Suetake, T. / Miura, A. / Spyracopoulos, L. / Kondo, H. / Tsuda, S.
#1: Journal: J.Biochem.(Tokyo) / Year: 1999
Title: Determination of the Solution Structure of the N-Domain Plus Linker of Antarctic Eel Pout Antifreeze Protein Rd3
Authors: Miura, K. / Ohgiya, S. / Hoshino, T. / Nemoto, N. / Odaira, M. / Nitta, K. / Tsuda, S.
#2: Journal: Nature / Year: 1996
Title: Structural Basis for the Binding of a Globular Antifreeze Protein to Ice
Authors: Jia, Z. / Deluca, C.I. / Chao, H. / Davies, P.L.
#3: 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.
#4: Journal: Biochim.Biophys.Acta / Year: 1995
Title: Antifreeze Peptide Heterogeneity in an Antarctic Eel Pout Includes an Unusually Large Major Variant Comprised of Two 7 kDa Type III Afps Linked in Tandem
Authors: Wang, X. / Devries, A.L. / Cheng, C.H.
History
DepositionMay 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ANTIFREEZE PROTEIN TYPE III)


Theoretical massNumber of molelcules
Total (without water)14,4901
Polymers14,4901
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)1 / 40AVERAGE
Representative

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Components

#1: Protein PROTEIN (ANTIFREEZE PROTEIN TYPE III) / RD3


Mass: 14490.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pachycara brachycephalum (Antarctic eelpout)
Tissue: BLOOD PLASMA / Description: SYNTHETIC GENE / Variant: RD3 / Plasmid: PKK223-3UC / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P35753

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
12115N-1H HSQC
13113C-1H HSQC 15N-TOCSYHSQC
14115N-NOESYHSQC
15115N-HNHA
161HNCA
171HN(CA)CB
181CBCA(CO)NH
191C(CO)NH
1101HC(CO)NH
1111(H)CCH-TOCSY
1121MOTHER-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C/15N-LABELED RD3

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditionspH: 6.7 / Pressure: 1 atm / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: SA / Software ordinal: 1
NMR ensembleConformer selection criteria: AVERAGE / Conformers calculated total number: 40 / Conformers submitted total number: 1

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