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- PDB-9i1o: The MK-RSL - sulfato-terphen[3]arene complex, C121 form -

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Basic information

Entry
Database: PDB / ID: 9i1o
TitleThe MK-RSL - sulfato-terphen[3]arene complex, C121 form
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Beta-propeller / Enzyme / Lectin / Fucose-binding
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / : / beta-D-fructopyranose / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsIfeagwu, M.C. / Mockler, N.M. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2025
Title: N-Terminal Protein Complexation and Assembly with a Triangular Sulfated Macrocycle
Authors: Ifeagwu, M.C. / Guo, L. / Mockler, N.M. / Dong, M. / Li, C. / Crowley, P.B.
History
DepositionJan 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
D: Fucose-binding lectin protein
E: Fucose-binding lectin protein
F: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,48319
Polymers59,4416
Non-polymers4,04213
Water11,331629
1
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8029
Polymers29,7213
Non-polymers1,0816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-18 kcal/mol
Surface area12020 Å2
2
D: Fucose-binding lectin protein
E: Fucose-binding lectin protein
F: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,68110
Polymers29,7213
Non-polymers2,9617
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-11 kcal/mol
Surface area13130 Å2
Unit cell
Length a, b, c (Å)167.523, 45.994, 70.159
Angle α, β, γ (deg.)90.000, 108.240, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-287-

HOH

21A-288-

HOH

31C-242-

HOH

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Components

#1: Protein
Fucose-binding lectin protein


Mass: 9906.859 Da / Num. of mol.: 6 / Mutation: M0, S1K
Source method: isolated from a genetically manipulated source
Details: Fucose-binding lectin protein, Putative fucose-binding lectin protein
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: E7Z57_08365, HF909_06975, LBW55_09125, RUN39_v1_50103 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1
#2: Sugar
ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-A1IZO / sulfato-terphen[3]arene complex


Mass: 1879.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C57H42O48S12 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 26, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.64→44.66 Å / Num. obs: 61998 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.046 / Rrim(I) all: 0.122 / Net I/σ(I): 11
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2828 / CC1/2: 0.777 / Rpim(I) all: 0.357 / Rrim(I) all: 0.869 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS1.20.1_4487data reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→44.66 Å / SU ML: 0.162 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1942 3113 5.02 %
Rwork0.1558 58874 -
obs0.1578 61987 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.41 Å2
Refinement stepCycle: LAST / Resolution: 1.64→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 261 629 5078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914606
X-RAY DIFFRACTIONf_angle_d0.95246369
X-RAY DIFFRACTIONf_chiral_restr0.0617694
X-RAY DIFFRACTIONf_plane_restr0.0072741
X-RAY DIFFRACTIONf_dihedral_angle_d12.98131438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.670.28461130.23082421X-RAY DIFFRACTION91.09
1.67-1.70.26961390.20972671X-RAY DIFFRACTION100
1.7-1.720.28661320.20672667X-RAY DIFFRACTION100
1.72-1.760.25231230.19552698X-RAY DIFFRACTION99.93
1.76-1.790.25011580.1932627X-RAY DIFFRACTION99.96
1.79-1.830.2621230.18142687X-RAY DIFFRACTION100
1.83-1.870.21721500.17562676X-RAY DIFFRACTION100
1.87-1.910.22241570.17082672X-RAY DIFFRACTION99.96
1.91-1.960.2151540.16362640X-RAY DIFFRACTION100
1.96-2.010.211250.15752703X-RAY DIFFRACTION100
2.01-2.070.22681410.15892671X-RAY DIFFRACTION100
2.07-2.140.19861420.15562663X-RAY DIFFRACTION100
2.14-2.210.1821410.15442683X-RAY DIFFRACTION99.96
2.21-2.30.20561420.15312679X-RAY DIFFRACTION99.96
2.3-2.410.18181370.15952712X-RAY DIFFRACTION100
2.41-2.530.19541600.16212658X-RAY DIFFRACTION100
2.53-2.690.20541350.1582718X-RAY DIFFRACTION100
2.69-2.90.18761280.15642709X-RAY DIFFRACTION100
2.9-3.190.18311610.15232668X-RAY DIFFRACTION100
3.19-3.650.17621400.13462721X-RAY DIFFRACTION100
3.65-4.60.14881420.12472745X-RAY DIFFRACTION100
4.6-44.660.16311700.14622785X-RAY DIFFRACTION99.9

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