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- PDB-8c9y: The MK-RSL - sulfonato-calix[8]arene complex, H32 form -

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Basic information

Entry
Database: PDB / ID: 8c9y
TitleThe MK-RSL - sulfonato-calix[8]arene complex, H32 form
ComponentsPutative fucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Macrocycle / Calixarene / Lectin
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / beta-D-fructopyranose / sulfonato-calix[8]arene / Putative fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsMockler, N.M. / Ramberg, K. / Crowley, P.B.
Funding support Ireland, 3items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation Ireland12/RC/2275_P2 Ireland
Irish Research CouncilGOIPG/2021/333 Ireland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Protein-macrocycle polymorphism: crystal form IV of the Ralstonia solanacearum lectin-sulfonato-calix[8]arene complex.
Authors: Mockler, N.M. / Ramberg, K.O. / Crowley, P.B.
History
DepositionJan 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4307
Polymers9,9071
Non-polymers3,5236
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.933, 75.933, 113.851
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Components on special symmetry positions
IDModelComponents
11A-101-

EVB

21A-101-

EVB

31A-101-

EVB

41A-101-

EVB

51A-279-

HOH

61A-286-

HOH

71A-289-

HOH

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Components

#1: Protein Putative fucose-binding lectin protein


Mass: 9906.859 Da / Num. of mol.: 1 / Mutation: M0, S1K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: CMR15_11270 / Production host: Escherichia coli (E. coli) / References: UniProt: D8NA05
#2: Chemical ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 2 / 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: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.49 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M tri-sodium citrate

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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: Mar 30, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.18→56.94 Å / Num. obs: 41673 / % possible obs: 100 % / Redundancy: 15.2 % / Biso Wilson estimate: 13.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.015 / Rrim(I) all: 0.058 / Net I/σ(I): 20.4
Reflection shellResolution: 1.18→1.2 Å / Rmerge(I) obs: 1.225 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2023 / CC1/2: 0.697 / Rpim(I) all: 0.464 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→43.04 Å / SU ML: 0.1092 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0512
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1754 2117 5.08 %
Rwork0.1631 39537 -
obs0.1636 41654 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.09 Å2
Refinement stepCycle: LAST / Resolution: 1.18→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 228 93 1019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047961
X-RAY DIFFRACTIONf_angle_d0.76891368
X-RAY DIFFRACTIONf_chiral_restr0.0771115
X-RAY DIFFRACTIONf_plane_restr0.0051281
X-RAY DIFFRACTIONf_dihedral_angle_d9.3236163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.210.26561570.29092591X-RAY DIFFRACTION99.82
1.21-1.240.25081470.252571X-RAY DIFFRACTION100
1.24-1.270.2731350.22922649X-RAY DIFFRACTION99.96
1.27-1.310.20411400.2052604X-RAY DIFFRACTION99.96
1.31-1.350.1841500.18552602X-RAY DIFFRACTION99.96
1.35-1.40.15031270.16752616X-RAY DIFFRACTION99.85
1.4-1.450.18551600.1652598X-RAY DIFFRACTION100
1.46-1.520.18421440.15792640X-RAY DIFFRACTION99.78
1.52-1.60.18081270.1592608X-RAY DIFFRACTION99.96
1.6-1.70.18221390.15852632X-RAY DIFFRACTION99.96
1.7-1.830.15451410.16092633X-RAY DIFFRACTION100
1.83-2.020.16611380.15172656X-RAY DIFFRACTION100
2.02-2.310.18611430.16222669X-RAY DIFFRACTION99.96
2.31-2.910.17681240.17282695X-RAY DIFFRACTION100
2.91-43.040.15591450.14462773X-RAY DIFFRACTION99.83

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