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- PDB-3nla: NMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF A... -

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Basic information

Entry
Database: PDB / ID: 3nla
TitleNMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF ANTARCTIC EEL POUT ANTIFREEZE PROTEIN RD3, 40 STRUCTURES
ComponentsANTIFREEZE PROTEIN RD3 TYPE III
KeywordsANTIFREEZE / ANTIFREEZE PROTEIN / 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 speciesLycodichthys dearborni (Antarctic eel pout)
MethodSOLUTION NMR / SA
AuthorsMiura, K. / Ohgiya, S. / Hoshino, T. / Nemoto, N. / Hikichi, K. / Tsuda, S.
Citation
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.
#1: 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.
#2: 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.
#3: 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
DepositionFeb 24, 1998Processing site: BNL
Revision 1.0Feb 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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 RD3 TYPE III


Theoretical massNumber of molelcules
Total (without water)7,8851
Polymers7,8851
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)40 / 100LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein ANTIFREEZE PROTEIN RD3 TYPE III / RD3-NL


Mass: 7885.328 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN WITH A LINKER PORTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycodichthys dearborni (Antarctic eel pout)
Tissue: BLOOD PLASMA / Organ: BLOOD / 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
111DQFCOSY
121TOCSY
131NOESY
14115N-HSQC
15115N TOCSYHSQC
16115N-NOESYHSQC
17115N-HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING DOUBLE-RESONANCE NMR SPECTROSCOPY ON 15N-LABELED RD3-NL

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Sample preparation

Sample conditionspH: 6.7 / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
JEOL JNM AJEOLJNM A5002

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: SA / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 40

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