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- PDB-1m8n: Choristoneura Fumiferana (Spruce Budworm) Antifreeze Protein Isof... -

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Basic information

Entry
Database: PDB / ID: 1m8n
TitleChoristoneura Fumiferana (Spruce Budworm) Antifreeze Protein Isoform 501
ComponentsAntifreeze protein isoform 501
KeywordsANTIFREEZE PROTEIN / LEFT-HANDED BETA-HELIX
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 / Antifreeze protein isoform 501
Function and homology information
Biological speciesChoristoneura fumiferana (eastern spruce budworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLeinala, E.K. / Davies, P.L. / Jia, Z.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: A beta-helical antifreeze protein isoform with increased activity: structural and functional insights
Authors: Leinala, E.K. / Davies, P.L. / Doucet, D. / Tyshenko, M.G. / Walker, V.K. / Jia, Z.
History
DepositionJul 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antifreeze protein isoform 501
B: Antifreeze protein isoform 501
C: Antifreeze protein isoform 501
D: Antifreeze protein isoform 501


Theoretical massNumber of molelcules
Total (without water)50,1884
Polymers50,1884
Non-polymers00
Water2,414134
1
A: Antifreeze protein isoform 501


Theoretical massNumber of molelcules
Total (without water)12,5471
Polymers12,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Antifreeze protein isoform 501


Theoretical massNumber of molelcules
Total (without water)12,5471
Polymers12,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Antifreeze protein isoform 501


Theoretical massNumber of molelcules
Total (without water)12,5471
Polymers12,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Antifreeze protein isoform 501


Theoretical massNumber of molelcules
Total (without water)12,5471
Polymers12,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.900, 57.400, 70.130
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Antifreeze protein isoform 501


Mass: 12546.899 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Choristoneura fumiferana (eastern spruce budworm)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9GSA6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG-4000, iso-propanol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
PH range low: 5.6 / PH range high: 4.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 %PEG40001reservoir
220 %isopropanol1reservoir
3100 mMsodium citrate1reservoirpH4.8-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2001
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 12991 / Num. obs: 11129 / % possible obs: 82.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.45→2.6 Å / % possible all: 69.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 12991 / % possible obs: 85.7 % / Num. measured all: 567512 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 71.3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Theoretical model based on pdb 1L0S

1l0s


Resolution: 2.45→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.291 1106 random
Rwork0.221 --
all-11129 -
obs-10750 -
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 0 134 3558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond lengths0.006
X-RAY DIFFRACTIONbond angles1.3
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.3

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