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- PDB-9hbd: The RSL - phosphonato-calix[6]arene cocrystal structure, pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 9hbd
TitleThe RSL - phosphonato-calix[6]arene cocrystal structure, pH 4.0
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: 1.09 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
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,65410
Polymers19,4672
Non-polymers5,1878
Water5,837324
1
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3275
Polymers9,7341
Non-polymers2,5944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3275
Polymers9,7341
Non-polymers2,5944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.991, 82.991, 157.427
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-325-

HOH

21A-345-

HOH

31A-350-

HOH

41A-376-

HOH

51B-408-

HOH

61B-423-

HOH

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Components

#1: Protein Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 9733.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, 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.: 4 / Source method: obtained synthetically / Formula: C42H42O24P6 / 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.: 4 / 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.: 324 / 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: 2.18 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 18 % PEG 3350, 0.1 M sodium citrate pH 4.0

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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: 1.09→52.48 Å / Num. obs: 82159 / % possible obs: 93.9 % / Redundancy: 16.5 % / Biso Wilson estimate: 12.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.7
Reflection shellResolution: 1.09→1.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.585 / Num. unique obs: 2190 / CC1/2: 0.452

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→52.48 Å / SU ML: 0.1123 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1994 4081 4.98 %
Rwork0.1841 77877 -
obs0.1848 81958 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.21 Å2
Refinement stepCycle: LAST / Resolution: 1.09→52.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 336 324 2034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041776
X-RAY DIFFRACTIONf_angle_d0.862522
X-RAY DIFFRACTIONf_chiral_restr0.078228
X-RAY DIFFRACTIONf_plane_restr0.0058264
X-RAY DIFFRACTIONf_dihedral_angle_d7.1821436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10.4195610.31941267X-RAY DIFFRACTION44.99
1.1-1.110.309850.29721626X-RAY DIFFRACTION57.01
1.11-1.130.31361090.30421917X-RAY DIFFRACTION66.93
1.13-1.140.31961230.2842145X-RAY DIFFRACTION76.42
1.14-1.160.29371350.28072398X-RAY DIFFRACTION85.52
1.16-1.170.27361200.25572706X-RAY DIFFRACTION94.04
1.17-1.190.30981470.24252770X-RAY DIFFRACTION97.43
1.19-1.210.30261580.23692790X-RAY DIFFRACTION98.3
1.21-1.230.22041630.23562783X-RAY DIFFRACTION99.19
1.23-1.250.24181630.22312851X-RAY DIFFRACTION99.97
1.25-1.270.23541440.21622842X-RAY DIFFRACTION99.93
1.28-1.30.22431240.21762877X-RAY DIFFRACTION99.97
1.3-1.330.22031470.20792819X-RAY DIFFRACTION99.83
1.33-1.350.22221380.1982865X-RAY DIFFRACTION99.83
1.35-1.390.20941420.19662875X-RAY DIFFRACTION99.9
1.39-1.420.2021420.19522888X-RAY DIFFRACTION99.97
1.42-1.460.20251460.20022843X-RAY DIFFRACTION99.97
1.46-1.50.1911510.19922853X-RAY DIFFRACTION100
1.5-1.550.21311520.18712838X-RAY DIFFRACTION99.97
1.55-1.610.19871510.19242862X-RAY DIFFRACTION99.97
1.61-1.670.18151440.18182877X-RAY DIFFRACTION99.97
1.67-1.750.2171450.18412866X-RAY DIFFRACTION99.97
1.75-1.840.19641590.19352866X-RAY DIFFRACTION99.97
1.84-1.950.19811510.18352883X-RAY DIFFRACTION99.97
1.95-2.10.20551410.17972899X-RAY DIFFRACTION99.87
2.11-2.320.18821590.17992891X-RAY DIFFRACTION99.97
2.32-2.650.23031650.18872879X-RAY DIFFRACTION100
2.65-3.340.18091550.17542936X-RAY DIFFRACTION99.94
3.34-52.480.15381610.14042965X-RAY DIFFRACTION97.44

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