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- PDB-8q6b: The RSL-D32N - sulfonato-calix[8]arene complex, I23 form, citrate... -

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Basic information

Entry
Database: PDB / ID: 8q6b
TitleThe RSL-D32N - sulfonato-calix[8]arene complex, I23 form, citrate pH 4.0, obtained by cross-seeding
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / biomaterials / beta-propeller / crystal engineering / molecular glue
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: 1.52 Å
AuthorsFlood, R.J. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
Citation
Journal: 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.
#1: Journal: J Am Chem Soc / Year: 2021
Title: Facile Fabrication of Protein-Macrocycle Frameworks.
Authors: Ramberg, K.O. / Engilberge, S. / Skorek, T. / Crowley, P.B.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionAug 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7468
Polymers9,7331
Non-polymers5,0137
Water1,17165
1
A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,23724
Polymers29,1983
Non-polymers15,03921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area8460 Å2
ΔGint-13 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.160, 112.160, 112.160
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-260-

HOH

21A-261-

HOH

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Components

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


Mass: 9732.577 Da / Num. of mol.: 1 / Mutation: D32N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, HF909_06975, HXP36_18875, RSP795_21825, RSP822_19650, 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.: 3 / 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.: 2 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100 mM tri-Sodium citrate pH 4.0, 1000 mM Ammonium 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: Nov 11, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.52→45.79 Å / Num. obs: 36271 / % possible obs: 100 % / Redundancy: 34.4 % / Biso Wilson estimate: 18.66 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.117 / Net I/σ(I): 22.6
Reflection shellResolution: 1.52→1.55 Å / Num. unique obs: 1805 / CC1/2: 0.748 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1_4487refinement
autoPROCdata processing
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→39.65 Å / SU ML: 0.1251 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.183 1861 5.13 %
Rwork0.1769 34407 -
obs0.1772 36268 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.47 Å2
Refinement stepCycle: LAST / Resolution: 1.52→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms688 0 324 65 1077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541055
X-RAY DIFFRACTIONf_angle_d0.76381525
X-RAY DIFFRACTIONf_chiral_restr0.0553114
X-RAY DIFFRACTIONf_plane_restr0.0047361
X-RAY DIFFRACTIONf_dihedral_angle_d11.7638187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.560.25981600.2332613X-RAY DIFFRACTION100
1.56-1.610.19271380.2022618X-RAY DIFFRACTION100
1.61-1.660.1821080.18862661X-RAY DIFFRACTION100
1.66-1.720.18971520.18072611X-RAY DIFFRACTION100
1.72-1.790.21541600.17362610X-RAY DIFFRACTION100
1.79-1.870.20531710.1852614X-RAY DIFFRACTION100
1.87-1.960.17131250.17112620X-RAY DIFFRACTION100
1.96-2.090.18281300.17182687X-RAY DIFFRACTION100
2.09-2.250.20961470.2012605X-RAY DIFFRACTION100
2.25-2.470.2181440.19992679X-RAY DIFFRACTION100
2.48-2.830.2021340.21062650X-RAY DIFFRACTION100
2.83-3.560.19121410.18142678X-RAY DIFFRACTION100
3.57-39.650.13691510.13872761X-RAY DIFFRACTION99.9

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