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- PDB-1n4i: Solution structure of spruce budworm antifreeze protein at 5 degr... -

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Basic information

Entry
Database: PDB / ID: 1n4i
TitleSolution structure of spruce budworm antifreeze protein at 5 degrees celsius
Componentsthermal hysteresis 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. / Gagne, S.M. / Spyracopoulos, L. / Jia, Z. / Davies, P.L. / Sykes, B.D.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Spruce Budworm Antifreeze Protein: Changes in Structure and Dynamics at Low Temperature
Authors: Graether, S.P. / Gagne, S.M. / Spyracopoulos, L. / Jia, Z. / Davies, P.L. / Sykes, B.D.
#1: 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. / Walkver, V.K. / Jia, Z. / Sykes, B.D. / Davies, P.L.
History
DepositionOct 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 1.4Oct 30, 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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Assembly

Deposited unit
A: thermal hysteresis 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)25 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein thermal hysteresis 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)
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 15N-separated NOESY
1213D 13C/15N-separated NOESY
1312D NOESY
NMR detailsText: This structure was determined using standard 3D homonuclear techniques.

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Sample preparation

DetailsContents: Uniform lableing with 13C, 15N / Solvent system: 90% H2O, 10% D20
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: ambient / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY8001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerrefinement
NMRPipe97.231.15.18Delaglioprocessing
PIPP1997Garrettdata analysis
VNMR6.1CVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
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: 25

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