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

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Basic information

Entry
Database: PDB / ID: 7bwx
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: 1.904 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
D: Ice-binding protein isoform1a
E: Ice-binding protein isoform1a
F: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,99720
Polymers133,6606
Non-polymers1,33714
Water27,6351534
1
A: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4693
Polymers22,2771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-22 kcal/mol
Surface area7750 Å2
MethodPISA
2
B: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4693
Polymers22,2771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7790 Å2
MethodPISA
3
C: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5654
Polymers22,2771
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7780 Å2
MethodPISA
4
D: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4693
Polymers22,2771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-22 kcal/mol
Surface area7810 Å2
MethodPISA
5
E: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4693
Polymers22,2771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area7750 Å2
MethodPISA
6
F: Ice-binding protein isoform1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5574
Polymers22,2771
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.427, 207.281, 100.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Ice-binding protein isoform1a


Mass: 22276.666 Da / Num. of mol.: 6 / Mutation: N55D
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1534 / 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: 3.38 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.1 M HEPES-NaOH pH 8.6, 0.95 M ammonium sulfate and 0.1 M lithium sulfate

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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 S 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→47.62 Å / Num. obs: 141990 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.045 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 20446 / CC1/2: 0.888 / Rpim(I) all: 0.197 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WP9

3wp9


Resolution: 1.904→47.62 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.002 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1641 7119 5.016 %Random selection
Rwork0.1351 ---
all0.137 ---
obs0.1366 141916 99.889 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.482 Å2
Baniso -1Baniso -2Baniso -3
1--0.481 Å2-0 Å2-0 Å2
2--0.916 Å20 Å2
3----0.435 Å2
Refinement stepCycle: LAST / Resolution: 1.904→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8442 0 72 1534 10048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138614
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177764
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.61711812
X-RAY DIFFRACTIONr_angle_other_deg1.5381.56217926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20451212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99426.122294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.629151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.676156
X-RAY DIFFRACTIONr_chiral_restr0.0760.21278
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021626
X-RAY DIFFRACTIONr_nbd_refined0.2040.21441
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.27418
X-RAY DIFFRACTIONr_nbtor_refined0.1590.24353
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24276
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.21123
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.140.25
X-RAY DIFFRACTIONr_nbd_other0.0990.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.230.241
X-RAY DIFFRACTIONr_mcbond_it1.9511.8464866
X-RAY DIFFRACTIONr_mcbond_other1.9471.8464865
X-RAY DIFFRACTIONr_mcangle_it2.9592.756072
X-RAY DIFFRACTIONr_mcangle_other2.9592.7516073
X-RAY DIFFRACTIONr_scbond_it3.0752.1533748
X-RAY DIFFRACTIONr_scbond_other3.0742.1543749
X-RAY DIFFRACTIONr_scangle_it4.5353.1185740
X-RAY DIFFRACTIONr_scangle_other4.5343.1195741
X-RAY DIFFRACTIONr_lrange_it6.66125.2279592
X-RAY DIFFRACTIONr_lrange_other6.14723.6789026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.904-1.9530.2165340.1949787X-RAY DIFFRACTION99.1927
1.953-2.0070.1955260.1749584X-RAY DIFFRACTION100
2.007-2.0650.2024930.169396X-RAY DIFFRACTION99.9899
2.065-2.1290.1774750.1519078X-RAY DIFFRACTION99.9895
2.129-2.1980.174610.1418855X-RAY DIFFRACTION99.9785
2.198-2.2760.1734600.1348525X-RAY DIFFRACTION99.9889
2.276-2.3610.1694210.1268250X-RAY DIFFRACTION99.9885
2.361-2.4580.1624460.1267979X-RAY DIFFRACTION99.9881
2.458-2.5670.163960.1247602X-RAY DIFFRACTION100
2.567-2.6920.1693850.1247323X-RAY DIFFRACTION99.9741
2.692-2.8380.1713690.1266961X-RAY DIFFRACTION100
2.838-3.010.1513180.1256631X-RAY DIFFRACTION99.9856
3.01-3.2170.1643430.1366201X-RAY DIFFRACTION99.9694
3.217-3.4750.1542930.1365839X-RAY DIFFRACTION99.9674
3.475-3.8060.1462640.1265356X-RAY DIFFRACTION99.9289
3.806-4.2550.1362650.1174853X-RAY DIFFRACTION99.9219
4.255-4.9110.1272190.1084317X-RAY DIFFRACTION99.6923
4.911-6.0120.151950.1333687X-RAY DIFFRACTION99.7687
6.012-8.4880.1861630.1552895X-RAY DIFFRACTION99.8368
8.488-47.620.196930.1841678X-RAY DIFFRACTION98.663

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