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- PDB-8x1l: Crystal structure of S96C/L132C mutant of FfIBP -

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Basic information

Entry
Database: PDB / ID: 8x1l
TitleCrystal structure of S96C/L132C 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 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 8, 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

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Assembly

Deposited unit
A: Ice-binding protein


Theoretical massNumber of molelcules
Total (without water)25,7371
Polymers25,7371
Non-polymers00
Water1,856103
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)69.060, 69.060, 178.350
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-400-

HOH

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Components

#1: Protein Ice-binding protein


Mass: 25736.971 Da / Num. of mol.: 1 / Mutation: S96C, L132C
Source method: isolated from a genetically manipulated source
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.: 103 / 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: 4.13 Å3/Da / Density % sol: 70.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium citrate 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 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→29.877 Å / Num. obs: 30097 / % possible obs: 100 % / Redundancy: 25.8 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.9
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2183 / 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→29.877 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.016 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.251 1484 4.931 %
Rwork0.2265 28613 -
all0.228 --
obs-30097 99.924 %
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: 39.659 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 2→29.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 0 103 1655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131574
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171481
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.6322147
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5673432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2935215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77224.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23915250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.883154
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_refined0.1980.2295
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.21332
X-RAY DIFFRACTIONr_nbtor_refined0.1530.2777
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2783
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0620.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.010.23
X-RAY DIFFRACTIONr_nbd_other0.2360.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.23
X-RAY DIFFRACTIONr_mcbond_it4.2734.148863
X-RAY DIFFRACTIONr_mcbond_other4.2644.145862
X-RAY DIFFRACTIONr_mcangle_it5.1496.1841077
X-RAY DIFFRACTIONr_mcangle_other5.156.1861078
X-RAY DIFFRACTIONr_scbond_it4.4724.44710
X-RAY DIFFRACTIONr_scbond_other4.3814.429708
X-RAY DIFFRACTIONr_scangle_it6.46.5041070
X-RAY DIFFRACTIONr_scangle_other6.3896.5011070
X-RAY DIFFRACTIONr_lrange_it7.32650.8881680
X-RAY DIFFRACTIONr_lrange_other7.34750.8631676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3341190.3272064X-RAY DIFFRACTION99.9542
2.052-2.1080.342860.3022016X-RAY DIFFRACTION99.9049
2.108-2.1690.35910.3161999X-RAY DIFFRACTION99.9522
2.169-2.2360.373910.3271916X-RAY DIFFRACTION100
2.236-2.3090.3621040.3121836X-RAY DIFFRACTION100
2.309-2.390.334930.2871804X-RAY DIFFRACTION100
2.39-2.480.303970.2691729X-RAY DIFFRACTION100
2.48-2.5810.348800.2771675X-RAY DIFFRACTION100
2.581-2.6960.317840.2711602X-RAY DIFFRACTION100
2.696-2.8270.288870.2651538X-RAY DIFFRACTION100
2.827-2.980.314810.2611486X-RAY DIFFRACTION99.9362
2.98-3.160.258710.2521408X-RAY DIFFRACTION100
3.16-3.3780.295750.2461311X-RAY DIFFRACTION100
3.378-3.6480.272720.2181235X-RAY DIFFRACTION100
3.648-3.9950.206530.1781140X-RAY DIFFRACTION99.9163
3.995-4.4650.133540.1671062X-RAY DIFFRACTION100
4.465-5.1520.179500.148934X-RAY DIFFRACTION100
5.152-6.3010.225430.182813X-RAY DIFFRACTION100
6.301-8.8740.144280.185657X-RAY DIFFRACTION100
8.874-29.8770.247250.224388X-RAY DIFFRACTION96.0465

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