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- PDB-8x0z: Crystal structure of A101C/A120C mutant of FfIBP -

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Basic information

Entry
Database: PDB / ID: 8x0z
TitleCrystal structure of A101C/A120C mutant of FfIBP
ComponentsIce-binding protein
KeywordsANTIFREEZE PROTEIN / ice-binding protein / Flavobacterium frigoris PS1 / ice recrystallization / thermal hysteresis
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: 2.1 Å
AuthorsNam, Y. / Do, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other governmentKIMST 20200610 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2024
Title: Engineered ice-binding protein (FfIBP) shows increased stability and resistance to thermal and chemical denaturation compared to the wildtype.
Authors: Nam, Y. / Nguyen, D.L. / Hoang, T. / Kim, B. / Lee, J.H. / Do, H.
History
DepositionNov 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ice-binding protein


Theoretical massNumber of molelcules
Total (without water)25,7951
Polymers25,7951
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8330 Å2
Unit cell
Length a, b, c (Å)69.230, 69.230, 178.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

21A-388-

HOH

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Components

#1: Protein Ice-binding protein


Mass: 25795.051 Da / Num. of mol.: 1 / Mutation: A101C, A120C
Source method: isolated from a genetically manipulated source
Details: A101C/A120C double mutant of FfIBP / Source: (gene. exp.) Flavobacterium frigoris PS1 (bacteria) / Gene: HJ01_03463 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H7FWB6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate pH 4.4, 3 M 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: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.25 Å / Num. obs: 26223 / % possible obs: 100 % / Redundancy: 25.5 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 39.2
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 2099 / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.25 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.493 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.158
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2811 1328 5.066 %
Rwork0.2538 24888 -
all0.255 --
obs-26216 99.905 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.894 Å2
Baniso -1Baniso -2Baniso -3
1-0.609 Å20 Å20 Å2
2--0.609 Å2-0 Å2
3----1.219 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 0 159 1715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131579
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171486
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.6312154
X-RAY DIFFRACTIONr_angle_other_deg1.3461.5673445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2795215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75524.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62715253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.156154
X-RAY DIFFRACTIONr_chiral_restr0.0850.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02291
X-RAY DIFFRACTIONr_nbd_refined0.1980.2297
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21373
X-RAY DIFFRACTIONr_nbtor_refined0.1530.2762
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.22
X-RAY DIFFRACTIONr_nbd_other0.190.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.26
X-RAY DIFFRACTIONr_mcbond_it3.5423.73863
X-RAY DIFFRACTIONr_mcbond_other3.5163.727862
X-RAY DIFFRACTIONr_mcangle_it4.5095.5631077
X-RAY DIFFRACTIONr_mcangle_other4.5135.5661078
X-RAY DIFFRACTIONr_scbond_it3.8053.981716
X-RAY DIFFRACTIONr_scbond_other3.7893.974714
X-RAY DIFFRACTIONr_scangle_it5.3785.8481077
X-RAY DIFFRACTIONr_scangle_other5.3795.8471077
X-RAY DIFFRACTIONr_lrange_it6.63846.0531706
X-RAY DIFFRACTIONr_lrange_other6.58845.7131683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.3381030.2691781X-RAY DIFFRACTION99.7881
2.155-2.2140.329880.2741747X-RAY DIFFRACTION100
2.214-2.2780.332870.2771729X-RAY DIFFRACTION100
2.278-2.3480.392890.2591648X-RAY DIFFRACTION100
2.348-2.4250.261810.2441618X-RAY DIFFRACTION100
2.425-2.510.272790.2561574X-RAY DIFFRACTION100
2.51-2.6040.318830.2781491X-RAY DIFFRACTION100
2.604-2.710.353630.2681482X-RAY DIFFRACTION100
2.71-2.8310.301710.2591408X-RAY DIFFRACTION100
2.831-2.9690.427730.2881350X-RAY DIFFRACTION100
2.969-3.1290.29740.2751278X-RAY DIFFRACTION100
3.129-3.3180.261760.2731209X-RAY DIFFRACTION99.9222
3.318-3.5470.275670.2371140X-RAY DIFFRACTION100
3.547-3.830.215610.2281084X-RAY DIFFRACTION100
3.83-4.1940.238560.224991X-RAY DIFFRACTION100
4.194-4.6870.258410.219931X-RAY DIFFRACTION99.8972
4.687-5.4080.229630.239798X-RAY DIFFRACTION100
5.408-6.6140.245370.248707X-RAY DIFFRACTION100
6.614-9.3110.304180.267578X-RAY DIFFRACTION100
9.311-29.250.38180.32344X-RAY DIFFRACTION95.2632

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