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- PDB-6z5p: The RSL-R8 - sulfonato-calix[8]arene complex, P3 form, TRIS-HCl pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 6z5p
TitleThe RSL-R8 - sulfonato-calix[8]arene complex, P3 form, TRIS-HCl pH 8.5
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / calixarene / protein framework / cage / crystal engineering / molecular glue / synthetic receptor / macrocycle / biomaterial / supercharged
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / beta-D-fructopyranose / sulfonato-calix[8]arene / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsRamberg, K. / Skorek, T. / 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 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 / 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
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,85112
Polymers19,7762
Non-polymers4,07610
Water5,368298
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)35,77718
Polymers29,6633
Non-polymers6,11415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7270 Å2
ΔGint-50 kcal/mol
Surface area14570 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)35,77718
Polymers29,6633
Non-polymers6,11415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7290 Å2
ΔGint-51 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.061, 60.061, 59.595
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

21A-321-

HOH

31B-308-

HOH

41B-326-

HOH

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#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
#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.: 4
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, 304 molecules

#2: 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.09 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M TRIS-HCl pH 8.5, 1.3 M Ammonium sulfate, 0.05 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: 1.42→59.6 Å / Num. obs: 45137 / % possible obs: 99 % / Redundancy: 10.5 % / CC1/2: 1 / Rpim(I) all: 0.13 / Rrim(I) all: 0.42 / Net I/σ(I): 23.8
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2253 / CC1/2: 0.826 / Rpim(I) all: 0.329 / Rrim(I) all: 1.092 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6STH

6sth


Resolution: 1.42→59.6 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 2.87 / Phase error: 14.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1587 2055 4.56 %
Rwork0.1309 43050 -
obs0.1321 45105 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.14 Å2 / Biso mean: 32.3275 Å2 / Biso min: 15.72 Å2
Refinement stepCycle: final / Resolution: 1.42→59.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 262 299 1958
Biso mean--44.81 47.09 -
Num. residues----176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.42-1.450.1941860.20012910299698
1.45-1.490.19881250.16872857298298
1.49-1.530.18011420.13972844298698
1.53-1.570.13991610.13122826298798
1.57-1.620.15481380.12722844298299
1.62-1.680.1521260.1252851297799
1.68-1.750.15421780.12552816299499
1.75-1.830.15651400.12462881302199
1.83-1.920.13421520.10882870302299
1.93-2.050.1331300.11622869299999
2.05-2.20.12341420.12562878302099
2.2-2.430.16921060.134129323038100
2.43-2.780.20951300.155328873017100
2.78-3.50.19691520.138128853037100
3.5-52.010.12951470.120329003047100

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