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- PDB-6z5g: The RSL - sulfonato-calix[8]arene complex, I23 form, citrate pH 4... -

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Basic information

Entry
Database: PDB / ID: 6z5g
TitleThe RSL - sulfonato-calix[8]arene complex, I23 form, citrate pH 4.0, solved by S-SAD
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: 1.278 Å
AuthorsEngilberge, S. / Ramberg, K. / Crowley, P.B.
Funding support Ireland, Switzerland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Swiss National Science Foundation200021-182369 Switzerland
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 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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)13,0776
Polymers9,7341
Non-polymers3,3435
Water3,351186
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)39,23118
Polymers29,2013
Non-polymers10,03015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area7590 Å2
ΔGint-22 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.795, 103.795, 103.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

21A-367-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
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
#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.: 186 / 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: 2.4 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 100 mM tri-Sodium citrate pH 4.0, 800 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.278→73.394 Å / Num. obs: 48052 / % possible obs: 100 % / Redundancy: 39.8 % / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.013 / Net I/σ(I): 29.9
Reflection shellResolution: 1.278→1.3 Å / Rmerge(I) obs: 2.071 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2392 / CC1/2: 0.774 / Rpim(I) all: 0.345 / % 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: 1.278→42.374 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1728 2371 4.93 %
Rwork0.1553 45677 -
obs0.1562 48048 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.46 Å2 / Biso mean: 21.9842 Å2 / Biso min: 9.66 Å2
Refinement stepCycle: final / Resolution: 1.278→42.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms687 0 216 203 1106
Biso mean--23.52 36.23 -
Num. residues----90
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005953
X-RAY DIFFRACTIONf_angle_d0.781361
X-RAY DIFFRACTIONf_chiral_restr0.079113
X-RAY DIFFRACTIONf_plane_restr0.005283
X-RAY DIFFRACTIONf_dihedral_angle_d10.64295
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.2782-1.30430.24431520.23252657
1.3043-1.33270.22621540.22312635
1.3327-1.36370.25021420.21452692
1.3637-1.39780.24191340.21842636
1.3978-1.43560.20021500.19762665
1.4356-1.47780.18791330.18292694
1.4778-1.52550.16411590.17662637
1.5255-1.580.16911260.16542685
1.58-1.64330.1621410.16562661
1.6433-1.71810.17441370.15412715
1.7181-1.80870.1791320.16212660
1.8087-1.9220.16241340.15422684
1.922-2.07040.18491630.15252677
2.0704-2.27870.18211330.16052678
2.2787-2.60840.17751410.16132727
2.6084-3.28620.15851120.14992751
3.2862-42.3740.1491280.12742823

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