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- PDB-9hbf: The MK-RSL - phosphonato-calix[6]arene cocrystal structure -

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Basic information

Entry
Database: PDB / ID: 9hbf
TitleThe MK-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 / 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. / 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)11,2084
Polymers9,9071
Non-polymers1,3013
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-0 kcal/mol
Surface area6390 Å2
Unit cell
Length a, b, c (Å)87.973, 87.973, 87.973
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-297-

HOH

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Components

#1: Protein Fucose-binding lectin protein


Mass: 9906.859 Da / Num. of mol.: 1 / Mutation: Met0, S1K
Source method: isolated from a genetically manipulated source
Details: Ralstonia solanacearum lectin with a Met-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: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.58 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.26 M Ammonium sulfate, 0.1 M TRIS pH 8.5, 0.2 m Lithium sulfate

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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: Jun 4, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.19→35.91 Å / Num. obs: 36569 / % possible obs: 99.7 % / Redundancy: 31.7 % / Biso Wilson estimate: 16.97 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.4
Reflection shellResolution: 1.19→1.21 Å / Rmerge(I) obs: 2.57 / Num. unique obs: 1728 / CC1/2: 0.351

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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→35.91 Å / SU ML: 0.1074 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2011 1862 5.12 %
Rwork0.183 34525 -
obs0.1839 36387 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.06 Å2
Refinement stepCycle: LAST / Resolution: 1.19→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 84 124 906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043816
X-RAY DIFFRACTIONf_angle_d0.80681136
X-RAY DIFFRACTIONf_chiral_restr0.0746108
X-RAY DIFFRACTIONf_plane_restr0.005130
X-RAY DIFFRACTIONf_dihedral_angle_d10.8154293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.220.31961380.30732363X-RAY DIFFRACTION89.07
1.22-1.250.25411360.27472650X-RAY DIFFRACTION99.96
1.25-1.290.29311230.26242712X-RAY DIFFRACTION100
1.3-1.340.26671490.25052621X-RAY DIFFRACTION99.96
1.34-1.390.25071560.22872651X-RAY DIFFRACTION100
1.4-1.460.23551810.22872606X-RAY DIFFRACTION100
1.46-1.540.20571250.21432711X-RAY DIFFRACTION100
1.54-1.630.19831260.19572660X-RAY DIFFRACTION100
1.63-1.760.23191590.21672679X-RAY DIFFRACTION100
1.76-1.930.23741380.20192673X-RAY DIFFRACTION100
1.93-2.210.20971380.1872696X-RAY DIFFRACTION100
2.21-2.790.1811410.1892712X-RAY DIFFRACTION100
2.79-35.910.17451520.14542791X-RAY DIFFRACTION99.9

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