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- PDB-9frn: The RSL-D46H - sulfonato-calix[8]arene complex, acetate pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 9frn
TitleThe RSL-D46H - sulfonato-calix[8]arene complex, acetate pH 4.0
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Assembly / Beta-propeller / Lectin / Trimer
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / beta-D-fructopyranose / sulfonato-calix[8]arene / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsFlood, R.J. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: Cryst Growth Des / Year: 2024
Title: Supramolecular Synthons in Protein-Ligand Frameworks.
Authors: Flood, R.J. / Mockler, N.M. / Thureau, A. / Malinska, M. / Crowley, P.B.
History
DepositionJun 19, 2024Deposition 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)66,66022
Polymers58,5406
Non-polymers8,12016
Water7,314406
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)36,30913
Polymers29,2703
Non-polymers7,03910
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-16 kcal/mol
Surface area14320 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)30,3519
Polymers29,2703
Non-polymers1,0816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-15 kcal/mol
Surface area11670 Å2
Unit cell
Length a, b, c (Å)47.222, 51.339, 69.472
Angle α, β, γ (deg.)83.590, 83.110, 67.940
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Fucose-binding lectin protein


Mass: 9756.621 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: D46H mutant of RSL / Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: E7Z57_08365, HF909_06975, LBW55_09125, RUN39_v1_50103 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1
#2: Chemical
ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.66 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 4 / Details: 20 mM sodium acetate pH 4.0 50 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.87→47.46 Å / Num. obs: 48037 / % possible obs: 97 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.94 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.086 / Net I/σ(I): 5.6
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2445 / CC1/2: 0.895 / Rpim(I) all: 0.256 / Rrim(I) all: 0.489 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→47.45 Å / SU ML: 0.2638 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.5891
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 2253 4.69 %
Rwork0.2103 45760 -
obs0.2121 48013 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.64 Å2
Refinement stepCycle: LAST / Resolution: 1.87→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 528 406 5074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534832
X-RAY DIFFRACTIONf_angle_d0.69986762
X-RAY DIFFRACTIONf_chiral_restr0.049684
X-RAY DIFFRACTIONf_plane_restr0.00461046
X-RAY DIFFRACTIONf_dihedral_angle_d7.9217762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.910.37791350.31252866X-RAY DIFFRACTION96.19
1.91-1.960.33091420.26842839X-RAY DIFFRACTION96.32
1.96-20.28631470.24772799X-RAY DIFFRACTION96.27
2-2.060.27161350.22272901X-RAY DIFFRACTION96.69
2.06-2.120.27581320.23082827X-RAY DIFFRACTION96.23
2.12-2.190.28591230.23052835X-RAY DIFFRACTION96.86
2.19-2.270.30751360.23422904X-RAY DIFFRACTION96.75
2.27-2.360.30071280.24062836X-RAY DIFFRACTION96.89
2.36-2.460.28991580.22722889X-RAY DIFFRACTION97.13
2.46-2.590.32671290.23372807X-RAY DIFFRACTION96.42
2.59-2.760.2491600.22142876X-RAY DIFFRACTION97.03
2.76-2.970.30021380.22462866X-RAY DIFFRACTION97.66
2.97-3.270.21911410.20142885X-RAY DIFFRACTION97.05
3.27-3.740.21481360.18352833X-RAY DIFFRACTION96.71
3.74-4.710.18921450.17562925X-RAY DIFFRACTION98.87
4.71-47.450.21831680.19022872X-RAY DIFFRACTION98.51

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