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- PDB-7ehk: Crystal structure of C107S mutant of FfIBP -

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Basic information

Entry
Database: PDB / ID: 7ehk
TitleCrystal structure of C107S mutant of FfIBP
ComponentsIce-binding protein
KeywordsANTIFREEZE PROTEIN / ice-binding protein / capping head region
Function / homologyIce-binding protein / Ice-binding-like / extracellular region / Ice-binding protein
Function and homology information
Biological speciesFlavobacterium frigoris PS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDo, H. / Lee, J.H.
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Importance of rigidity of ice-binding protein (FfIBP) for hyperthermal hysteresis activity and microbial survival.
Authors: Hwang, J. / Kim, B. / Lee, M.J. / Kim, E.J. / Cho, S.M. / Lee, S.G. / Han, S.J. / Kim, K. / Lee, J.H. / Do, H.
History
DepositionMar 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: 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: Ice-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8214
Polymers25,7151
Non-polymers1063
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area8210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.620, 69.620, 178.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

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Components

#1: Protein Ice-binding protein / Antifreeze protein / AFP / FfIBP


Mass: 25714.855 Da / Num. of mol.: 1 / Mutation: C107S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium frigoris PS1 (bacteria) / Strain: PS1 / Gene: HJ01_03463 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H7FWB6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 4.21 Å3/Da / Density % sol: 70.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium acetate pH 4.6, 3M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→29.4 Å / Num. obs: 30586 / % possible obs: 99.9 % / Redundancy: 26.2 % / Biso Wilson estimate: 44.88 Å2 / CC1/2: 0.99 / Net I/σ(I): 23.7
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2213 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
MxDC1.18.2_3874data collection
autoPROC1.18.2_3874data processing
Aimlessdata scaling
MOLREPphasing
PHENIX1.18.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NU2

4nu2


Resolution: 2→29.4 Å / SU ML: 0.2886 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.9264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 1501 4.91 %
Rwork0.228 29077 -
obs0.229 30578 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.16 Å2
Refinement stepCycle: LAST / Resolution: 2→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 3 91 1648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751575
X-RAY DIFFRACTIONf_angle_d0.99982148
X-RAY DIFFRACTIONf_chiral_restr0.0617271
X-RAY DIFFRACTIONf_plane_restr0.0068272
X-RAY DIFFRACTIONf_dihedral_angle_d13.5618222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.41211370.35882554X-RAY DIFFRACTION99.63
2.06-2.140.31121100.33722616X-RAY DIFFRACTION99.63
2.14-2.220.40121280.31792579X-RAY DIFFRACTION99.71
2.22-2.330.34011400.30672601X-RAY DIFFRACTION99.71
2.33-2.450.29511360.28712593X-RAY DIFFRACTION99.93
2.45-2.60.31071340.29152628X-RAY DIFFRACTION99.96
2.6-2.80.31641300.28882635X-RAY DIFFRACTION99.93
2.8-3.080.33791540.2882624X-RAY DIFFRACTION100
3.08-3.530.29261420.24232666X-RAY DIFFRACTION99.96
3.53-4.440.17691390.17392709X-RAY DIFFRACTION100
4.44-29.40.18591510.17582872X-RAY DIFFRACTION99.83

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