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- PDB-9hbg: The PK-RSL - phosphonato-calix[6]arene cocrystal structure -

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Basic information

Entry
Database: PDB / ID: 9hbg
TitleThe PK-RSL - phosphonato-calix[6]arene cocrystal structure
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Beta-propeller / lectin / trimer
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / phosphonato-calix[6]arene / beta-D-fructopyranose / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsMockler, N.M. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Irish Research CouncilGOIPG/2021/333 Ireland
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: Chemistry / Year: 2025
Title: Making and Breaking Supramolecular Synthons for Modular Protein Frameworks.
Authors: Mockler, N.M. / Raston, C.L. / Crowley, P.B.
History
DepositionNov 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3504
Polymers9,8731
Non-polymers1,4773
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint1 kcal/mol
Surface area6520 Å2
Unit cell
Length a, b, c (Å)88.377, 88.377, 88.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-292-

HOH

21A-320-

HOH

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Components

#1: Protein Fucose-binding lectin protein


Mass: 9872.778 Da / Num. of mol.: 1 / Mutation: Pro0, S1K
Source method: isolated from a genetically manipulated source
Details: Ralstonia solanacearum lectin with a Pro-Lys N-terminus
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.: 2 / 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
#3: Chemical ChemComp-7AZ / phosphonato-calix[6]arene


Mass: 1116.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H42O24P6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.1 M Di-ammonium hydrogen phosphate, 0.1 M 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: Nov 16, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.28→31.25 Å / Num. obs: 29915 / % possible obs: 100 % / Redundancy: 39 % / Biso Wilson estimate: 20 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 37.6
Reflection shellResolution: 1.28→1.298 Å / Rmerge(I) obs: 1.556 / Num. unique obs: 1478 / CC1/2: 0.827

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→31.25 Å / SU ML: 0.1699 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.6373
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2044 1487 4.97 %
Rwork0.1947 28427 -
obs0.1952 29914 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.61 Å2
Refinement stepCycle: LAST / Resolution: 1.28→31.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms697 0 96 120 913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054830
X-RAY DIFFRACTIONf_angle_d0.81081163
X-RAY DIFFRACTIONf_chiral_restr0.0734116
X-RAY DIFFRACTIONf_plane_restr0.0052130
X-RAY DIFFRACTIONf_dihedral_angle_d10.7904303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.320.38041190.30122559X-RAY DIFFRACTION100
1.32-1.360.29151450.2862558X-RAY DIFFRACTION99.96
1.36-1.420.30591560.27212536X-RAY DIFFRACTION100
1.42-1.480.30871510.2812565X-RAY DIFFRACTION100
1.48-1.560.22971560.25252558X-RAY DIFFRACTION100
1.56-1.660.23041070.25312580X-RAY DIFFRACTION100
1.66-1.790.27561500.24692576X-RAY DIFFRACTION100
1.79-1.970.27591020.24812612X-RAY DIFFRACTION100
1.97-2.250.2331620.21082576X-RAY DIFFRACTION100
2.25-2.830.24421090.20482641X-RAY DIFFRACTION100
2.84-31.250.1381300.14272666X-RAY DIFFRACTION98.69

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