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- PDB-1ezg: CRYSTAL STRUCTURE OF ANTIFREEZE PROTEIN FROM THE BEETLE, TENEBRIO... -

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Basic information

Entry
Database: PDB / ID: 1ezg
TitleCRYSTAL STRUCTURE OF ANTIFREEZE PROTEIN FROM THE BEETLE, TENEBRIO MOLITOR
ComponentsTHERMAL HYSTERESIS PROTEIN ISOFORM YL-1
KeywordsANTIFREEZE PROTEIN / insect antifreeze protein / thermal hysteresis / Tenebrio molitor / iodination / right-handed beta-helix / TmAFP
Function / homologyInsect antifreeze protein / Insect antifreeze protein motif / Insect cysteine-rich antifreeze protein / Insect antifreeze protein repeat / Pectate Lyase C-like / 3 Solenoid / extracellular region / Mainly Beta / Thermal hysteresis protein YL-1
Function and homology information
Biological speciesTenebrio molitor (yellow mealworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsLiou, Y.-C. / Tocilj, A. / Davies, P.L. / Jia, Z.
CitationJournal: Nature / Year: 2000
Title: Mimicry of ice structure by surface hydroxyls and water of a beta-helix antifreeze protein.
Authors: Liou, Y.C. / Tocilj, A. / Davies, P.L. / Jia, Z.
History
DepositionMay 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / 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: THERMAL HYSTERESIS PROTEIN ISOFORM YL-1
B: THERMAL HYSTERESIS PROTEIN ISOFORM YL-1


Theoretical massNumber of molelcules
Total (without water)16,7782
Polymers16,7782
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-8 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.832, 73.832, 53.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsIn solution, it is monomer. But it is a dimer in crystal.

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Components

#1: Protein THERMAL HYSTERESIS PROTEIN ISOFORM YL-1


Mass: 8389.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tenebrio molitor (yellow mealworm) / Description: LARVAE HEMOLYMPH / Gene: CDNA FROM FAT BODY LIBRARY / Plasmid: PET20B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O16119
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

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, sodium citra, cobalt chloridee, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
21.5 M1reservoirLi2SO4
3100 mMglycine-NaOH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.4→25 Å / Num. all: 133370 / Num. obs: 32557 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.208 / Num. unique all: 3086 / % possible all: 95.6
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SHELXL-97refinement
RefinementResolution: 1.4→5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1996 3072 Random
Rwork0.1605 --
all0.16 133370 -
obs0.16 32557 -
Refinement stepCycle: LAST / Resolution: 1.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 0 0 1106
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d2.154
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.154

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