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- PDB-9gr3: The MK-RSL - sulfonato-calix[4]arene complex -

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Basic information

Entry
Database: PDB / ID: 9gr3
TitleThe MK-RSL - sulfonato-calix[4]arene complex
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Beta-propeller / lectin / trimer
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / beta-D-fructopyranose / Chem-T3Y / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsMockler, N.M. / Ramberg, K.O. / Flood, R.J. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Irish Research CouncilGOIPG/2021/333 Ireland
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: Biochemistry / Year: 2025
Title: N-Terminal Protein Binding and Disorder-to-Order Transition by a Synthetic Receptor.
Authors: Mockler, N.M. / Ramberg, K.O. / Flood, R.J. / Crowley, P.B.
History
DepositionSep 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,29111
Polymers29,7213
Non-polymers2,5708
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-18 kcal/mol
Surface area12710 Å2
Unit cell
Length a, b, c (Å)43.678, 74.046, 43.857
Angle α, β, γ (deg.)90.000, 119.468, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Fucose-binding lectin protein


Mass: 9906.859 Da / Num. of mol.: 3 / Mutation: Met0, S1K
Source method: isolated from a genetically manipulated source
Details: Met-Lys N-terminal extension / 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: Chemical ChemComp-T3Y / 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid / 5,11,17,23-tetra-sulphonato-calix[4]arene-25,26,27,28-tetrol


Mass: 744.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H24O16S4 / 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.: 6 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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.: 346 / 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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1 M di-ammonium hydrogen phosphate, 0.1M sodium acetate pH 4.5

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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: Jul 9, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.19→38.18 Å / Num. obs: 75076 / % possible obs: 96.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 12.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Net I/σ(I): 13.2
Reflection shellResolution: 1.19→1.21 Å / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3155 / CC1/2: 0.648 / Rpim(I) all: 0.373 / Rrim(I) all: 0.791

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→38.18 Å / SU ML: 0.1036 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.7257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1997 3574 4.76 %
Rwork0.1782 71470 -
obs0.1792 75044 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.51 Å2
Refinement stepCycle: LAST / Resolution: 1.19→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 168 346 2591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422326
X-RAY DIFFRACTIONf_angle_d0.77283228
X-RAY DIFFRACTIONf_chiral_restr0.0729344
X-RAY DIFFRACTIONf_plane_restr0.0067372
X-RAY DIFFRACTIONf_dihedral_angle_d10.4915803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.210.31981160.27682242X-RAY DIFFRACTION79.82
1.21-1.220.26381080.24942577X-RAY DIFFRACTION89.44
1.22-1.240.23641190.24152629X-RAY DIFFRACTION94.17
1.24-1.260.24721250.23082760X-RAY DIFFRACTION95.62
1.26-1.280.24881320.22422713X-RAY DIFFRACTION96.41
1.28-1.30.25711460.21162719X-RAY DIFFRACTION96.4
1.3-1.320.22821430.20312749X-RAY DIFFRACTION96.69
1.32-1.350.23571410.20332730X-RAY DIFFRACTION97.06
1.35-1.370.21271070.19892776X-RAY DIFFRACTION96.91
1.37-1.40.21951820.19662687X-RAY DIFFRACTION97.35
1.4-1.430.1991320.18912787X-RAY DIFFRACTION97.43
1.43-1.460.21931640.18482751X-RAY DIFFRACTION97.49
1.46-1.50.19691550.18152728X-RAY DIFFRACTION97.66
1.5-1.540.18891590.17652754X-RAY DIFFRACTION98.15
1.54-1.590.18721380.17182777X-RAY DIFFRACTION97.82
1.59-1.640.1817970.17122841X-RAY DIFFRACTION98.39
1.64-1.70.20211340.16472806X-RAY DIFFRACTION98.53
1.7-1.760.20651010.16932834X-RAY DIFFRACTION98.66
1.76-1.840.1841440.17312795X-RAY DIFFRACTION98.92
1.84-1.940.19391220.16682836X-RAY DIFFRACTION99
1.94-2.060.16591210.17392835X-RAY DIFFRACTION99.39
2.06-2.220.17741440.17292831X-RAY DIFFRACTION99.43
2.22-2.450.19732000.17432787X-RAY DIFFRACTION99.37
2.45-2.80.20371100.18252856X-RAY DIFFRACTION99.63
2.8-3.530.19261820.16572824X-RAY DIFFRACTION99.83
3.53-38.180.20181520.16872846X-RAY DIFFRACTION98.13

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