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- PDB-3vn3: Fungal antifreeze protein exerts hyperactivity by constructing an... -

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Basic information

Entry
Database: PDB / ID: 3vn3
TitleFungal antifreeze protein exerts hyperactivity by constructing an inequable beta-helix
ComponentsAntifreeze protein
KeywordsANTIFREEZE PROTEIN / right-handed beta-helix
Function / homologyIce-binding protein / Ice-binding-like / Ice-binding protein K3-B1
Function and homology information
Biological speciesTyphula ishikariensis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.95 Å
AuthorsKondo, H. / Xiao, N. / Hanada, Y. / Sugimoto, H. / Hoshino, T. / Garnham, C.P. / Davies, P.L. / Tsuda, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Ice-binding site of snow mold fungus antifreeze protein deviates from structural regularity and high conservation
Authors: Kondo, H. / Hanada, Y. / Sugimoto, H. / Hoshino, T. / Garnham, C.P. / Davies, P.L. / Tsuda, S.
History
DepositionDec 21, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antifreeze protein
B: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0509
Polymers44,6162
Non-polymers4347
Water14,682815
1
A: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5565
Polymers22,3081
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4944
Polymers22,3081
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.890, 41.630, 70.250
Angle α, β, γ (deg.)81.53, 83.13, 62.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Antifreeze protein


Mass: 22307.771 Da / Num. of mol.: 2 / Fragment: UNP residues 21-243 / Source method: isolated from a natural source / Source: (natural) Typhula ishikariensis (fungus) / Strain: BRB-1 / References: UniProt: Q76CE6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 815 / 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

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.1M Bis-Tris, 1.0M ammonium sulfate, 0.1M sodium chloride, pH 6.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.95→34.41 Å / Num. obs: 232289 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.9
Reflection shellResolution: 0.95→1 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2 / Num. unique all: 32714 / % possible all: 92

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 0.95→34.41 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.373 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.12948 11700 5 %RANDOM
Rwork0.11214 ---
obs0.11302 220586 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.482 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0.1 Å2-0.01 Å2
2---0.17 Å20.25 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 0.95→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 28 815 3971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223301
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9784538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7215477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76625.12282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.33315482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.036156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212396
X-RAY DIFFRACTIONr_mcbond_it1.4851.52235
X-RAY DIFFRACTIONr_mcangle_it2.21723623
X-RAY DIFFRACTIONr_scbond_it2.83831066
X-RAY DIFFRACTIONr_scangle_it3.8294.5898
X-RAY DIFFRACTIONr_rigid_bond_restr1.41633301
X-RAY DIFFRACTIONr_sphericity_free10.0333815
X-RAY DIFFRACTIONr_sphericity_bonded4.37233239
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 811 -
Rwork0.165 15561 -
obs-15561 90.78 %

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