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- PDB-2afp: THE SOLUTION STRUCTURE OF TYPE II ANTIFREEZE PROTEIN REVEALS A NE... -

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Basic information

Entry
Database: PDB / ID: 2afp
TitleTHE SOLUTION STRUCTURE OF TYPE II ANTIFREEZE PROTEIN REVEALS A NEW MEMBER OF THE LECTIN FAMILY
ComponentsPROTEIN (SEA RAVEN TYPE II ANTIFREEZE PROTEIN)
KeywordsANTIFREEZE PROTEIN / RECOMBINANT SEA RAVEN PROTEIN / SOLUTION BACKBONE FOLD / C-TYPE LECTIN
Function / homology
Function and homology information


carbohydrate binding / extracellular region
Similarity search - Function
Type-2 ice-structuring protein / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) ...Type-2 ice-structuring protein / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Type-2 ice-structuring protein
Similarity search - Component
Biological speciesHemitripterus americanus (sea raven)
MethodSOLUTION NMR / simulated annealing
AuthorsGronwald, W. / Loewen, M.C. / Lix, B. / Daugulis, A.J. / Sonnichsen, F.D. / Davies, P.L. / Sykes, B.D.
CitationJournal: Biochemistry / Year: 1998
Title: The solution structure of type II antifreeze protein reveals a new member of the lectin family.
Authors: Gronwald, W. / Loewen, M.C. / Lix, B. / Daugulis, A.J. / Sonnichsen, F.D. / Davies, P.L. / Sykes, B.D.
History
DepositionDec 14, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (SEA RAVEN TYPE II ANTIFREEZE PROTEIN)


Theoretical massNumber of molelcules
Total (without water)14,0031
Polymers14,0031
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)5 / 50GLOBAL ENERGY AND LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein PROTEIN (SEA RAVEN TYPE II ANTIFREEZE PROTEIN)


Mass: 14002.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SIX AMINO ACID HIS TAG WAS ADDED AT THE C-TERMINAL END TO FACILITATE RECOVERY OF THE SECRETED AFP FROM THE MEDIUM USING AFFINITY CHROMATOGRAPHY.
Source: (gene. exp.) Hemitripterus americanus (sea raven) / Organ: BLOOD / Plasmid: PPIC9-SRM-CTHT / Gene (production host): SRAFP GENE / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P05140
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D-TOCSY
1312D-NOESY
1413D-TOCSY-HSQC
1513D-NOESY-HSQC
1613D HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TWO AND THREE DIMENSIONAL NMR SPECTROSCOPY ON 15N-LABELED AND ON THE NATIVE SEA RAVEN ANTIFREEZE.

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Sample preparation

Sample conditionspH: 5.6 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY600 AND UNITYPLUS600 / Manufacturer: Varian / Model: UNITY600 AND UNITYPLUS600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
VNMRstructure solution
NMRPipestructure solution
PIPPstructure solution
X-PLOR3.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: IN THE CURRENT STRUCTURES ONLY THE GLOBAL FOLD OF THE MOLECULE IS PRESENTED. REFINED HIGH RESOLUTION SOLUTION STRUCTURES ARE NOT AVAILABLE AT THE MOMENT.
NMR ensembleConformer selection criteria: GLOBAL ENERGY AND LEAST RESTRAINT VIOLATION
Conformers calculated total number: 50 / Conformers submitted total number: 5

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