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- PDB-7bwy: Crystal structure of ice-binding protein from an Antarctic ascomy... -

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Basic information

Entry
Database: PDB / ID: 7bwy
TitleCrystal structure of ice-binding protein from an Antarctic ascomycete, Antarctomyces psychrotrophicus.
ComponentsIce-binding protein isoform1a
KeywordsANTIFREEZE PROTEIN / BETA-SOLENOID / RIGHT-HANDED BETA-HELIX
Function / homologyIce-binding protein / Ice-binding-like / Ice-binding protein isoform1a
Function and homology information
Biological speciesAntarctomyces psychrotrophicus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsYamauchi, A. / Arai, T. / Kondo, H. / Tsuda, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H02529 Japan
Japan Society for the Promotion of Science (JSPS)19K22989 Japan
CitationJournal: Biomolecules / Year: 2020
Title: An Ice-Binding Protein from an Antarctic Ascomycete Is Fine-Tuned to Bind to Specific Water Molecules Located in the Ice Prism Planes.
Authors: Yamauchi, A. / Arai, T. / Kondo, H. / Sasaki, Y.C. / Tsuda, S.
History
DepositionApr 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ice-binding protein isoform1a
B: Ice-binding protein isoform1a
C: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4277
Polymers67,0583
Non-polymers3684
Water5,729318
1
A: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4452
Polymers22,3531
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4452
Polymers22,3531
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5373
Polymers22,3531
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.311, 92.311, 222.669
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ice-binding protein isoform1a


Mass: 22352.762 Da / Num. of mol.: 3 / Mutation: N55D, S153Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Antarctomyces psychrotrophicus (fungus)
Gene: ibp / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A2Z6DSM4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 4.09 Å3/Da / Density % sol: 69.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Bis-Tris pH 7.0, 4.0 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.02→46.16 Å / Num. obs: 72989 / % possible obs: 99.9 % / Redundancy: 19.8 % / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.085 / Net I/σ(I): 21.1
Reflection shellResolution: 2.02→2.06 Å / Redundancy: 19.6 % / Rmerge(I) obs: 1.654 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4427 / CC1/2: 0.944 / Rpim(I) all: 0.382 / Rrim(I) all: 1.698 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BWX

7bwx


Resolution: 2.02→45.725 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 4.724 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 3649 5.005 %Random selection
Rwork0.1789 ---
all0.181 ---
obs0.1808 72904 99.874 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.926 Å2
Baniso -1Baniso -2Baniso -3
1-0.014 Å20.007 Å20 Å2
2--0.014 Å2-0 Å2
3----0.046 Å2
Refinement stepCycle: LAST / Resolution: 2.02→45.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 24 318 4581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0114319
X-RAY DIFFRACTIONr_angle_refined_deg2.0811.6135915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9125606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86326150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3215570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.136153
X-RAY DIFFRACTIONr_chiral_restr0.1440.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023225
X-RAY DIFFRACTIONr_nbd_refined0.2160.22003
X-RAY DIFFRACTIONr_nbtor_refined0.3270.23001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2343
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2760.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.29
X-RAY DIFFRACTIONr_mcbond_it5.8425.592433
X-RAY DIFFRACTIONr_mcangle_it7.0968.3263036
X-RAY DIFFRACTIONr_scbond_it7.2575.6831886
X-RAY DIFFRACTIONr_scangle_it8.1048.3752879
X-RAY DIFFRACTIONr_lrange_it8.94378.2816538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.0720.4182620.4245054X-RAY DIFFRACTION99.7748
2.072-2.1290.4212630.394901X-RAY DIFFRACTION99.6334
2.129-2.1910.3532480.3344832X-RAY DIFFRACTION99.8232
2.191-2.2580.332360.3074624X-RAY DIFFRACTION99.8152
2.258-2.3320.2942190.2784522X-RAY DIFFRACTION99.8946
2.332-2.4140.2942360.2554397X-RAY DIFFRACTION99.9137
2.414-2.5050.2942220.2464222X-RAY DIFFRACTION99.7531
2.505-2.6070.2842200.2264054X-RAY DIFFRACTION99.9766
2.607-2.7230.3132000.2253935X-RAY DIFFRACTION99.9758
2.723-2.8560.2691930.213766X-RAY DIFFRACTION100
2.856-3.010.2382030.193556X-RAY DIFFRACTION99.9468
3.01-3.1920.2221850.1843399X-RAY DIFFRACTION99.9721
3.192-3.4120.2331630.193206X-RAY DIFFRACTION99.9703
3.412-3.6850.1711680.1632959X-RAY DIFFRACTION99.9361
3.685-4.0360.2251440.1622763X-RAY DIFFRACTION99.9312
4.036-4.5110.1661250.142509X-RAY DIFFRACTION100
4.511-5.2060.1791250.1142229X-RAY DIFFRACTION100
5.206-6.370.165950.141922X-RAY DIFFRACTION99.9504
6.37-8.9790.172820.131518X-RAY DIFFRACTION100
8.979-45.7250.144600.14887X-RAY DIFFRACTION98.7487

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