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- PDB-6z60: The RSL - sulfonato-calix[8]arene complex, P213 form, CAPS pH 9.5 -

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Basic information

Entry
Database: PDB / ID: 6z60
TitleThe RSL - sulfonato-calix[8]arene complex, P213 form, CAPS pH 9.5
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / calixarene / protein framework / cage / crystal engineering / molecular glue / synthetic receptor / macrocycle / biomaterial
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Lipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-D-fructopyranose / sulfonato-calix[8]arene / Fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.166 Å
AuthorsRamberg, K. / Engilberge, S. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Facile Fabrication of Protein-Macrocycle Frameworks.
Authors: Ramberg, K.O. / Engilberge, S. / Skorek, T. / Crowley, P.B.
History
DepositionMay 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6795
Polymers9,7341
Non-polymers1,9464
Water2,036113
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)35,03815
Polymers29,2013
Non-polymers5,83812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7050 Å2
ΔGint-47 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.872, 63.872, 63.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-286-

HOH

21A-300-

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: Chemical ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: 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: isolated from a genetically manipulated source
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.23 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M CAPS pH 9.5, 1.6 M Ammonium sulfate, 0.2 M Lithium sulfate, 0.064 M sulfonato-calix[8]arene, 0.005 M D-fructose

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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: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.166→45.164 Å / Num. obs: 29919 / % possible obs: 100 % / Redundancy: 35.7 % / CC1/2: 1 / Rpim(I) all: 0.008 / Rrim(I) all: 0.048 / Net I/σ(I): 35.8
Reflection shellResolution: 1.166→1.19 Å / Redundancy: 15.5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1474 / CC1/2: 0.847 / Rpim(I) all: 0.232 / Rrim(I) all: 0.925 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9


Resolution: 1.166→45.164 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1681 1479 4.94 %
Rwork0.1513 28438 -
obs0.1521 29917 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.02 Å2 / Biso mean: 19.9331 Å2 / Biso min: 10.05 Å2
Refinement stepCycle: final / Resolution: 1.166→45.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 0 125 120 918
Biso mean--24.33 32.89 -
Num. residues----88
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005830
X-RAY DIFFRACTIONf_angle_d0.8891171
X-RAY DIFFRACTIONf_chiral_restr0.078113
X-RAY DIFFRACTIONf_plane_restr0.005198
X-RAY DIFFRACTIONf_dihedral_angle_d9.69260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.166-1.20320.21351270.18062585
1.2032-1.24620.20511420.15862523
1.2462-1.29610.17831140.14822583
1.2961-1.35510.15291410.14522550
1.3551-1.42650.17041290.13822570
1.4265-1.51590.1551150.14122583
1.5159-1.63290.15471650.14392538
1.6329-1.79730.19751310.15222579
1.7973-2.05740.14351380.14342615
2.0574-2.5920.1781350.15972603
2.592-45.1640.1661420.15172709

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