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- PDB-1eww: SOLUTION STRUCTURE OF SPRUCE BUDWORM ANTIFREEZE PROTEIN AT 30 DEG... -

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Basic information

Entry
Database: PDB / ID: 1eww
TitleSOLUTION STRUCTURE OF SPRUCE BUDWORM ANTIFREEZE PROTEIN AT 30 DEGREES CELSIUS
ComponentsANTIFREEZE PROTEIN
KeywordsANTIFREEZE PROTEIN / beta-helix / ice / insect
Function / homologyChoristoneura fumiferana antifreeze / Insect antifreeze protein superfamily / Choristoneura fumiferana antifreeze protein (CfAFP) / Insect antifreeze protein / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Mainly Beta / Thermal hysteresis protein
Function and homology information
Biological speciesChoristoneura fumiferana (eastern spruce budworm)
MethodSOLUTION NMR / simulated annealing
AuthorsGraether, S.P. / Kuiper, M.J. / Gagne, S.M. / Walker, V.K. / Jia, Z. / Sykes, B.D. / Davies, P.L.
Citation
Journal: Nature / Year: 2000
Title: Beta-helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect.
Authors: Graether, S.P. / Kuiper, M.J. / Gagne, S.M. / Walker, V.K. / Jia, Z. / Sykes, B.D. / Davies, P.L.
#1: Journal: NAT.BIOTECHNOL. / Year: 1997
Title: The Antifreeze Potential of the Spruce Budworm Thermal Hysteresis Protein.
Authors: Tyshenko, M.G. / Doucet, D. / Davies, P.L. / Walker, V.K.
History
DepositionApr 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)9,0681
Polymers9,0681
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 lowest energy
RepresentativeModel #10closest to the average

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Components

#1: Protein ANTIFREEZE PROTEIN


Mass: 9068.034 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Choristoneura fumiferana (eastern spruce budworm)
Tissue fraction: HEMOLYMPH / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GTP0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C/15N-separated NOESY
1213D 15N-separated NOESY
132HNHA
141HN(CA)CB
151CBCA(CO)NNH
161(H)CCH-TOCSY
1712D NOESY
1823D 15N-separated TOCSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1: U-15N/U-13C spruce budworm antifreeze protein, 18 mg/mL, 2: U-15N spruce budworm antifreeze protein, 18 mg/mL
Solvent system: 90% H2O, 10% D20
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian UNITYVarianUNITY6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
NMRPipe1.7Delaglioprocessing
PIPP4.2Garrettdata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 1014 NOE-derived distance constraints, 88 dihedral angle restraints, 59 carbon chemical shift restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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