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- PDB-6z5x: The RSL - sulfonato-calix[8]arene complex, P213 form, acetate pH 4.8 -

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Basic information

Entry
Database: PDB / ID: 6z5x
TitleThe RSL - sulfonato-calix[8]arene complex, P213 form, acetate pH 4.8
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: 1.14 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 7, 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

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7026
Polymers9,7341
Non-polymers1,9695
Water2,108117
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)35,10718
Polymers29,2013
Non-polymers5,90715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7460 Å2
ΔGint-85 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.056, 64.056, 64.056
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-300-

HOH

21A-306-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#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
#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

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Non-polymers , 4 types, 120 molecules

#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
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 34.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate pH 4.8, 2 M Ammonium sulfate, 0.064 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: 1.14→45.294 Å / Num. obs: 31827 / % possible obs: 98.7 % / Redundancy: 34.5 % / CC1/2: 1 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.016 / Net I/σ(I): 25.1
Reflection shellResolution: 1.14→1.159 Å / Rmerge(I) obs: 1.229 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1364 / CC1/2: 0.602 / Rpim(I) all: 0.331 / % possible all: 86.2

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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: 1.14→45.294 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1905 1628 5.12 %
Rwork0.1665 30198 -
obs0.1677 31826 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.48 Å2 / Biso mean: 15.2362 Å2 / Biso min: 6.47 Å2
Refinement stepCycle: final / Resolution: 1.14→45.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 0 126 119 918
Biso mean--17.57 27.18 -
Num. residues----88
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004837
X-RAY DIFFRACTIONf_angle_d0.8351181
X-RAY DIFFRACTIONf_chiral_restr0.076114
X-RAY DIFFRACTIONf_plane_restr0.005199
X-RAY DIFFRACTIONf_dihedral_angle_d9.8266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.14-1.1730.2391310.251219088
1.173-1.21090.25781330.2199242396
1.2109-1.25420.21331350.20262559100
1.2542-1.30440.19951450.19012482100
1.3044-1.36380.20931060.18382562100
1.3638-1.43570.21651240.17272542100
1.4357-1.52560.17871210.16682578100
1.5256-1.64340.18441250.15842535100
1.6434-1.80880.18811480.16362528100
1.8088-2.07060.17111700.15682541100
2.0706-2.60870.1931400.16572582100
2.6087-45.290.18261500.15232676100

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