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- PDB-7ddb: Crystal structure of fungal antifreeze protein with intermediate ... -

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Basic information

Entry
Database: PDB / ID: 7ddb
TitleCrystal structure of fungal antifreeze protein with intermediate activity
ComponentsAntifreeze protein
KeywordsANTIFREEZE PROTEIN / right-handed beta-helix / beta-solenoid / ice-binding protein / thermal hysteresis protein / ice-structuring protein
Function / homologyIce-binding protein / Ice-binding-like / Antifreeze protein
Function and homology information
Biological speciesTyphula ishikariensis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsKhan, N.M.M.U. / Arai, T. / Tsuda, S. / Kondo, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)KAKENHI JP20570118 Japan
CitationJournal: Sci Rep / Year: 2021
Title: Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity.
Authors: Khan, N.M.U. / Arai, T. / Tsuda, S. / Kondo, H.
History
DepositionOct 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,2535
Polymers44,1802
Non-polymers733
Water9,980554
1
A: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1142
Polymers22,0901
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area8610 Å2
MethodPISA
2
B: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1383
Polymers22,0901
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-9 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.790, 63.143, 102.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Antifreeze protein


Mass: 22089.811 Da / Num. of mol.: 2 / Mutation: T20Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Typhula ishikariensis (fungus) / Gene: K1-C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76CE7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.65 % / Description: thin plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH8.5, 30% (w/v) PEG 4000, 0.2M magnesium chloride
PH range: 8.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→49.68 Å / Num. obs: 41109 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 0.98 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.057 / Rrim(I) all: 0.201 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.7312.61.1372704221400.8490.3331.1862.399.9
9-49.639.10.14128883180.8780.0570.15410.293.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å49.63 Å
Translation3 Å49.63 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B5H

5b5h


Resolution: 1.72→49.68 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.005 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 1975 5 %RANDOM
Rwork0.2084 ---
obs0.2103 37745 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.39 Å2 / Biso mean: 10.893 Å2 / Biso min: 2.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--1.11 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 1.72→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 0 3 554 3669
Biso mean--16.1 20.23 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133174
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172989
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.6394348
X-RAY DIFFRACTIONr_angle_other_deg1.4371.5596921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8195448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22224.28684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47915458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.931154
X-RAY DIFFRACTIONr_chiral_restr0.0720.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023608
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02604
LS refinement shellResolution: 1.72→1.765 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 136 -
Rwork0.398 2753 -
all-2889 -
obs--99.86 %

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