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- PDB-8c9z: The RSL - sulfonato-calix[8]arene complex, H32 form, citrate pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 8c9z
TitleThe RSL - sulfonato-calix[8]arene complex, H32 form, citrate pH 6.0
ComponentsFucose-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 / 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
Irish Research CouncilGOIPG/2021/333 Ireland
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation Ireland12/RC/2275_P2 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: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2577
Polymers9,7341
Non-polymers3,5236
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.114, 76.114, 113.649
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-103-

EVB

21A-103-

EVB

31A-103-

EVB

41A-103-

EVB

51A-284-

HOH

61A-292-

HOH

71A-298-

HOH

81A-303-

HOH

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Components

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


Mass: 9733.562 Da / Num. of mol.: 1
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: 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
#3: 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
#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.: 103 / 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, hanging drop / pH: 6 / Details: 1.2 M tri-sodium citrate pH 6.0

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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: 1.18→57.02 Å / Num. obs: 41706 / % possible obs: 99.8 % / Redundancy: 17.3 % / Biso Wilson estimate: 13.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.016 / Rrim(I) all: 0.067 / Net I/σ(I): 19
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.304 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1963 / CC1/2: 0.622 / Rpim(I) all: 0.448 / % possible all: 96.3

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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: 0.1027 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3653
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1776 2106 5.05 %
Rwork0.1648 39585 -
obs0.1655 41691 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.93 Å2
Refinement stepCycle: LAST / Resolution: 1.18→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms687 0 228 103 1018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051957
X-RAY DIFFRACTIONf_angle_d0.85181366
X-RAY DIFFRACTIONf_chiral_restr0.0792115
X-RAY DIFFRACTIONf_plane_restr0.0054282
X-RAY DIFFRACTIONf_dihedral_angle_d8.8487164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.210.29481310.29162543X-RAY DIFFRACTION96.53
1.21-1.240.25051430.26372592X-RAY DIFFRACTION99.89
1.24-1.270.25451520.23922605X-RAY DIFFRACTION100
1.27-1.310.21751370.20522614X-RAY DIFFRACTION99.96
1.31-1.350.19561360.19262640X-RAY DIFFRACTION99.96
1.35-1.40.17041390.16622601X-RAY DIFFRACTION99.96
1.4-1.460.18231550.16682649X-RAY DIFFRACTION99.96
1.46-1.520.16621300.16322627X-RAY DIFFRACTION99.86
1.52-1.60.19651330.1622620X-RAY DIFFRACTION99.89
1.6-1.70.20241520.16282643X-RAY DIFFRACTION99.96
1.7-1.830.16471290.16532658X-RAY DIFFRACTION100
1.83-2.020.17171400.15622650X-RAY DIFFRACTION100
2.02-2.310.16591390.16022691X-RAY DIFFRACTION100
2.31-2.910.19431340.17122691X-RAY DIFFRACTION100
2.91-43.040.15231560.1442761X-RAY DIFFRACTION99.76

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