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- PDB-6sth: Highly cationic RSL-R8 in complex with sulfonato-calix[8]arene -

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Basic information

Entry
Database: PDB / ID: 6sth
TitleHighly cationic RSL-R8 in complex with sulfonato-calix[8]arene
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Molecular Glue / Calixarene / Supramolecular interactions / Sulfonato-calix[8]arene / ligand conformation
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / sulfonato-calix[8]arene / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.726 Å
AuthorsSkorek, T. / Engilberge, S. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: To Be Published
Title: Highly cationic RSL-R8 in complex with sulfonato-calix[8]arene
Authors: Skorek, T. / Engilberge, S. / Crowley, P.B.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,49912
Polymers19,7762
Non-polymers3,72410
Water5,224290
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)35,24918
Polymers29,6633
Non-polymers5,58515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area7490 Å2
ΔGint-59 kcal/mol
Surface area14050 Å2
MethodPISA
2
B: Fucose-binding lectin protein
hetero molecules

B: Fucose-binding lectin protein
hetero molecules

B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,24918
Polymers29,6633
Non-polymers5,58515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area7210 Å2
ΔGint-56 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.604, 60.604, 59.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-328-

HOH

31B-317-

HOH

41B-358-

HOH

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Components

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


Mass: 9887.790 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: RSP795_21825, RSP799_05830, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 3.18 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.6 mM RSL-R8 combined 33 mM sulfonato-calix[8]arene were crystallized using 0.1 M TRIS; pH 8.5, 1.26 M Ammonium sulfate, 0.2M Lithium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.73→59.3 Å / Num. obs: 25591 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 19.93 Å2 / Rpim(I) all: 0.062 / Rrim(I) all: 0.192 / Net I/σ(I): 13.7
Reflection shellResolution: 1.73→1.76 Å / Num. unique obs: 1242 / Rpim(I) all: 0.055 / Rrim(I) all: 1.691

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.726→39.302 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 1291 5.05 %RANDOM
Rwork0.1881 ---
obs0.1909 25550 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.726→39.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 238 290 1920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111680
X-RAY DIFFRACTIONf_angle_d1.2262348
X-RAY DIFFRACTIONf_dihedral_angle_d11.784838
X-RAY DIFFRACTIONf_chiral_restr0.067211
X-RAY DIFFRACTIONf_plane_restr0.008263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7257-1.79480.30511410.26552673X-RAY DIFFRACTION100
1.7948-1.87650.3041200.26312714X-RAY DIFFRACTION100
1.8765-1.97540.24751020.24112776X-RAY DIFFRACTION100
1.9754-2.09910.25391510.21282655X-RAY DIFFRACTION99
2.0991-2.26120.29921300.21492702X-RAY DIFFRACTION100
2.2612-2.48870.32461580.2192693X-RAY DIFFRACTION100
2.4887-2.84880.22951940.18112645X-RAY DIFFRACTION100
2.8488-3.58880.19241290.15052716X-RAY DIFFRACTION100
3.5888-39.31210.20471660.14712685X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 43.1291 Å / Origin y: 33.2013 Å / Origin z: 57.378 Å
111213212223313233
T0.2029 Å2-0.0022 Å2-0.0629 Å2-0.1715 Å20.0193 Å2--0.1605 Å2
L0.4599 °2-0.2804 °20.5313 °2-0.0287 °2-0.2459 °2--0.4402 °2
S0.1519 Å °-0.0375 Å °-0.2903 Å °-0.0525 Å °0.0582 Å °0.1611 Å °0.1849 Å °-0.067 Å °-0.0959 Å °
Refinement TLS groupSelection details: all

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