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- PDB-6z5q: The RSL - sulfonato-calix[8]arene complex, P3 form, acetate pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 6z5q
TitleThe RSL - sulfonato-calix[8]arene complex, P3 form, acetate pH 4.0
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / calixarene / protein framework / cage / crystal engineering / molecular glue / synthetic receptor / macrocycle / biomaterial
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate 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: 1.29 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 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
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,53512
Polymers19,4672
Non-polymers4,06810
Water7,692427
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)35,30318
Polymers29,2013
Non-polymers6,10215
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 area8200 Å2
ΔGint-16 kcal/mol
Surface area13670 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)35,30318
Polymers29,2013
Non-polymers6,10215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area8060 Å2
ΔGint-13 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.851, 59.851, 64.631
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-350-

HOH

21A-379-

HOH

31B-353-

HOH

41B-380-

HOH

51B-413-

HOH

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Components

#1: Protein Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 9733.562 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar
ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.29 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 4
Details: 0.02 M sodium acetate, 0.05 M NaCl, 0.01 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: Jan 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.29→51.83 Å / Num. obs: 64914 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Rrim(I) all: 0.078 / Net I/σ(I): 13.5
Reflection shellResolution: 1.29→1.32 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3257 / CC1/2: 0.951 / Rpim(I) all: 0.222 / Rrim(I) all: 0.689 / % possible all: 100

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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: 2BT9

2bt9


Resolution: 1.29→51.83 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2.35 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1649 3377 5.21 %
Rwork0.1364 61468 -
obs0.1379 64845 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.44 Å2 / Biso mean: 21.2167 Å2 / Biso min: 10.62 Å2
Refinement stepCycle: final / Resolution: 1.29→51.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 264 430 2068
Biso mean--22.53 34.13 -
Num. residues----180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.29-1.310.26411380.204425842722
1.31-1.330.207860.183926222708
1.33-1.350.20281120.171925262638
1.35-1.370.17491530.157925942747
1.37-1.40.17731460.148425172663
1.4-1.420.20311800.147325782758
1.42-1.450.19551220.139625572679
1.45-1.480.14351340.138725532687
1.48-1.510.2111000.136325912691
1.51-1.550.16291880.128625592747
1.55-1.590.20751080.130225732681
1.59-1.630.1571440.129225542698
1.63-1.680.13021240.128825912715
1.68-1.730.18091460.126725362682
1.73-1.790.1411680.133825272695
1.79-1.860.16131300.132225812711
1.86-1.950.18131200.137825832703
1.95-2.050.16691590.137725412700
2.05-2.180.18431960.137124782674
2.18-2.350.15621400.142425722712
2.35-2.580.14381680.139925692737
2.58-2.960.15591640.139925222686
2.96-3.720.15921250.129825772702
3.72-27.420.1631260.126525832709

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