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- PDB-6z5w: The RSL - sulfonato-calix[8]arene complex, P213 form, MES pH 6.8 -

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Basic information

Entry
Database: PDB / ID: 6z5w
TitleThe RSL - sulfonato-calix[8]arene complex, P213 form, MES pH 6.8
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: 1.187 Å
AuthorsEngilberge, S. / Ramberg, K. / 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 / pdbx_unobs_or_zero_occ_residues
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
Water2,306128
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 operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area7030 Å2
ΔGint-48 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.826, 63.826, 63.826
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-298-

HOH

21A-314-

HOH

31A-327-

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.: 128 / 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: 35.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.8, 2.4 M Ammonium sulfate, 0.04 M sulfonato-calix[8]arene

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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 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.187→45.132 Å / Num. obs: 28303 / % possible obs: 100 % / Redundancy: 36.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.021 / Net I/σ(I): 19
Reflection shellResolution: 1.187→1.207 Å / Redundancy: 19.7 % / Rmerge(I) obs: 1.427 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1395 / CC1/2: 0.794 / Rpim(I) all: 0.328 / % 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: 1.187→45.132 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 1523 5.38 %
Rwork0.1666 26779 -
obs0.1672 28302 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.12 Å2 / Biso mean: 15.7184 Å2 / Biso min: 6.67 Å2
Refinement stepCycle: final / Resolution: 1.187→45.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 0 125 132 930
Biso mean--18.86 29.13 -
Num. residues----87
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006826
X-RAY DIFFRACTIONf_angle_d0.8921164
X-RAY DIFFRACTIONf_chiral_restr0.076112
X-RAY DIFFRACTIONf_plane_restr0.005197
X-RAY DIFFRACTIONf_dihedral_angle_d9.983257
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.187-1.2250.20191470.21492381
1.225-1.26870.22251430.20112409
1.2687-1.31950.19291420.1912401
1.3195-1.37960.19011720.18122389
1.3796-1.45230.18811170.172421
1.4523-1.54330.16381350.16722406
1.5433-1.66250.16551120.15932471
1.6625-1.82980.1941300.16462449
1.8298-2.09460.1891310.15672449
2.0946-2.63890.17431530.17152451
2.6389-45.1320.16161410.15682552

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