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- PDB-9gr4: The MKA-RSL - sulfonato-calix[4]arene complex -

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Basic information

Entry
Database: PDB / ID: 9gr4
TitleThe MKA-RSL - sulfonato-calix[4]arene complex
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Beta-propeller / lectin / trimer
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / beta-D-fructopyranose / Chem-T3Y / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsMockler, N.M. / Ramberg, K.O. / Flood, R.J. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Irish Research CouncilGOIPG/2021/333 Ireland
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: Biochemistry / Year: 2025
Title: N-Terminal Protein Binding and Disorder-to-Order Transition by a Synthetic Receptor.
Authors: Mockler, N.M. / Ramberg, K.O. / Flood, R.J. / Crowley, P.B.
History
DepositionSep 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
E: Fucose-binding lectin protein
F: Fucose-binding lectin protein
D: Fucose-binding lectin protein
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,26421
Polymers59,8686
Non-polymers4,39615
Water14,340796
1
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
E: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,50411
Polymers29,9343
Non-polymers2,5708
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-19 kcal/mol
Surface area12810 Å2
2
F: Fucose-binding lectin protein
D: Fucose-binding lectin protein
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,75910
Polymers29,9343
Non-polymers1,8267
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-19 kcal/mol
Surface area12000 Å2
Unit cell
Length a, b, c (Å)44.048, 73.548, 75.893
Angle α, β, γ (deg.)90.000, 90.394, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Fucose-binding lectin protein


Mass: 9977.938 Da / Num. of mol.: 6 / Mutation: Met-1, Lys0, S1A
Source method: isolated from a genetically manipulated source
Details: Met-Lys-Ala N-terminal extension / 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.: 12 / 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-T3Y / 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid / 5,11,17,23-tetra-sulphonato-calix[4]arene-25,26,27,28-tetrol


Mass: 744.741 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H24O16S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 0.15 M di-sodium DL-malate pH 7.0

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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: Jul 9, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.077→75.891 Å / Num. obs: 176082 / % possible obs: 84.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 9.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 22.1
Reflection shellResolution: 1.077→1.095 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2849 / CC1/2: 0.863 / Rpim(I) all: 0.244 / Rrim(I) all: 0.362 / % possible all: 27.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→38.21 Å / SU ML: 0.0742 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.7092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1755 9059 5.15 %
Rwork0.1618 167000 -
obs0.1625 176059 84.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.52 Å2
Refinement stepCycle: LAST / Resolution: 1.08→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 288 796 5260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00384638
X-RAY DIFFRACTIONf_angle_d0.77186429
X-RAY DIFFRACTIONf_chiral_restr0.0739695
X-RAY DIFFRACTIONf_plane_restr0.0063750
X-RAY DIFFRACTIONf_dihedral_angle_d10.23741579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.090.3271810.2461705X-RAY DIFFRACTION25.75
1.09-1.10.2264990.22892156X-RAY DIFFRACTION32.27
1.1-1.120.25691440.21452516X-RAY DIFFRACTION38.67
1.12-1.130.22421740.19673066X-RAY DIFFRACTION46.63
1.13-1.140.21111690.19883406X-RAY DIFFRACTION52.01
1.14-1.160.1922600.19233817X-RAY DIFFRACTION58.26
1.16-1.180.20262380.18314217X-RAY DIFFRACTION64.96
1.18-1.190.19262700.18184853X-RAY DIFFRACTION73.43
1.19-1.210.2072750.18385487X-RAY DIFFRACTION83.74
1.21-1.230.17643210.18486157X-RAY DIFFRACTION93.05
1.23-1.250.19422650.17696364X-RAY DIFFRACTION95.96
1.25-1.280.17983580.17536362X-RAY DIFFRACTION96.69
1.28-1.30.2033310.17326431X-RAY DIFFRACTION96.82
1.3-1.330.17944120.17256305X-RAY DIFFRACTION97
1.33-1.360.18623560.1726390X-RAY DIFFRACTION97.39
1.36-1.390.17653340.17356415X-RAY DIFFRACTION97.42
1.39-1.420.18443140.16996487X-RAY DIFFRACTION97.74
1.42-1.460.18663750.17136405X-RAY DIFFRACTION97.76
1.46-1.50.1823270.16666526X-RAY DIFFRACTION98.17
1.5-1.550.17943600.16386443X-RAY DIFFRACTION98.31
1.55-1.610.17253710.16226466X-RAY DIFFRACTION98.46
1.61-1.670.18343480.15736514X-RAY DIFFRACTION98.66
1.67-1.750.16483940.16246502X-RAY DIFFRACTION98.81
1.75-1.840.18444490.16416456X-RAY DIFFRACTION99.15
1.84-1.960.1763300.1586566X-RAY DIFFRACTION99.37
1.96-2.110.17583760.15826582X-RAY DIFFRACTION99.57
2.11-2.320.17343530.15746616X-RAY DIFFRACTION99.66
2.32-2.650.17973260.16346621X-RAY DIFFRACTION99.71
2.65-3.340.1673250.15156673X-RAY DIFFRACTION99.72
3.34-38.210.1463240.14286496X-RAY DIFFRACTION95.83

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