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- PDB-9i1n: The MK-RSL - sulfato-terphen[3]arene complex, P63 form, citrate pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 9i1n
TitleThe MK-RSL - sulfato-terphen[3]arene complex, P63 form, citrate pH 4.0
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Beta-propeller / Enzyme / Lectin / Fucose-binding
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / : / beta-D-fructopyranose / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsIfeagwu, M.C. / Mockler, N.M. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2025
Title: N‐Terminal Protein Complexation and Assembly with a Triangular Sulfated Macrocycle.
Authors: Ifeagwu, M.C. / Guo, L. / Mockler, N.M. / Dong, M. / Li, C. / Crowley, P.B.
History
DepositionJan 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: 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

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Assembly

Deposited unit
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1474
Polymers9,9071
Non-polymers2,2403
Water1,53185
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)36,44112
Polymers29,7213
Non-polymers6,7209
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7700 Å2
ΔGint-15 kcal/mol
Surface area15180 Å2
Unit cell
Length a, b, c (Å)43.526, 43.526, 85.907
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21A-270-

HOH

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Components

#1: Protein Fucose-binding lectin protein


Mass: 9906.859 Da / Num. of mol.: 1 / Mutation: M0, S1K
Source method: isolated from a genetically manipulated source
Details: Fucose-binding lectin protein, Putative fucose-binding lectin protein
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-A1IZO / sulfato-terphen[3]arene complex


Mass: 1879.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C57H42O48S12 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.99 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1.2 M tri-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: Oct 26, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.696→37.695 Å / Num. obs: 10257 / % possible obs: 99.9 % / Redundancy: 18.9 % / Biso Wilson estimate: 15.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.023 / Rrim(I) all: 0.102 / Net I/σ(I): 19.9
Reflection shellResolution: 1.696→1.725 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 505 / CC1/2: 0.971 / Rpim(I) all: 0.205 / Rrim(I) all: 0.81 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS1.20.1_4487data reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→37.69 Å / SU ML: 0.1382 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1925 498 4.87 %
Rwork0.1562 9719 -
obs0.1578 10217 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 141 85 924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0186886
X-RAY DIFFRACTIONf_angle_d1.3241251
X-RAY DIFFRACTIONf_chiral_restr0.0732118
X-RAY DIFFRACTIONf_plane_restr0.0108135
X-RAY DIFFRACTIONf_dihedral_angle_d21.6085129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.870.27911270.20432399X-RAY DIFFRACTION98.75
1.87-2.140.17291360.15212409X-RAY DIFFRACTION99.73
2.14-2.690.22821380.17692424X-RAY DIFFRACTION99.73
2.69-37.690.1583970.13792487X-RAY DIFFRACTION99.85

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