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- PDB-6stz: Crystal structure of dimethylated RSLex - cucurbituril free form -

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Basic information

Entry
Database: PDB / ID: 6stz
TitleCrystal structure of dimethylated RSLex - cucurbituril free form
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / cucurbituril / molecular glue / crystal engineering
Function / homology
Function and homology information


carbohydrate 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 / Fucose-binding lectin protein / Fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsGuagnini, F. / Engilberge, S. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Engineered assembly of a protein-cucurbituril biohybrid.
Authors: Guagnini, F. / Engilberge, S. / Ramberg, K.O. / Perez, J. / Crowley, P.B.
History
DepositionSep 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
C: Fucose-binding lectin protein
D: Fucose-binding lectin protein
E: Fucose-binding lectin protein
F: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,24918
Polymers59,0876
Non-polymers2,16212
Water14,610811
1
A: Fucose-binding lectin protein
D: Fucose-binding lectin protein
E: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6249
Polymers29,5433
Non-polymers1,0816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-16 kcal/mol
Surface area11730 Å2
MethodPISA
2
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
F: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6249
Polymers29,5433
Non-polymers1,0816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-17 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.948, 43.948, 207.273
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Fucose-binding lectin protein


Mass: 9847.815 Da / Num. of mol.: 6 / Mutation: N79K, T82Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: rsl, RUN215_v1_180133 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4WQH1, UniProt: Q8XXK6*PLUS
#2: 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.: 12
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 811 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.98 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 100 mM BIS-TRIS pH 5.5, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.14→69.09 Å / Num. obs: 163813 / % possible obs: 99.8 % / Redundancy: 9.4 % / Biso Wilson estimate: 8.1 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.057 / Rrim(I) all: 0.179 / Net I/σ(I): 8.7 / Num. measured all: 1540149 / Scaling rejects: 1020
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.14-1.26.30.67149650236750.7550.2830.7292.898.8
3.6-69.0910.60.1215531452190.9930.0390.12717.1100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9 polyalanine

2bt9


Resolution: 1.14→69.09 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.04 / SU Rfree Blow DPI: 0.042 / SU Rfree Cruickshank DPI: 0.04
RfactorNum. reflection% reflectionSelection details
Rfree0.198 8163 4.99 %RANDOM
Rwork0.173 ---
obs0.174 163612 99.8 %-
Displacement parametersBiso max: 110.39 Å2 / Biso mean: 13.68 Å2 / Biso min: 4.91 Å2
Baniso -1Baniso -2Baniso -3
1-1.9447 Å20 Å20 Å2
2--1.9447 Å20 Å2
3----3.8894 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: final / Resolution: 1.14→69.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 2335 811 7281
Biso mean--12.59 24.29 -
Num. residues----270
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1342SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes703HARMONIC5
X-RAY DIFFRACTIONt_it4575HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion620SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6094SEMIHARMONIC6
X-RAY DIFFRACTIONt_bond_d4575HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6396HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion5.62
X-RAY DIFFRACTIONt_other_torsion11.84
LS refinement shellResolution: 1.14→1.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2516 174 5.32 %
Rwork0.2443 3099 -
all0.2447 3273 -
obs--94.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9754-0.4477-0.03151.44340.04330.1651-0.00740.00820.0273-0.03750.0294-0.17130.01010.0298-0.022-0.0268-0.00910.01040.0034-0.0098-0.02637.878213.45254.0582
21.18990.576-0.19910.7659-0.20250.4960.08430.02940.16340.0737-0.0070.106-0.1252-0.013-0.07730.02820.00620.0311-0.0278-0.0009-0.02867.770238.757639.1588
31.36150.4164-0.4180.8893-0.13580.4369-0.05580.0842-0.1467-0.02080.0245-0.01840.0312-0.05210.0313-0.0045-0.00780.0137-0.0125-0.0193-0.03094.99919.934637.126
41.67080.28020.05390.6992-0.07830-0.01710.061-0.1908-0.02780.02320.0180.0124-0.0005-0.0061-0.0168-0.00380.0085-0.0003-0.0081-0.0102-9.27525.4832.4471
50.90170.00480.02550.82980.22050.10390.01940.00690.072-0.0426-0.00120.0062-0.0295-0.0113-0.0182-0.0053-0.00610.00260.01150.005-0.0354-7.639124.94492.8806
61.2754-0.1139-0.42470.8732-0.08490.6651-0.02030.0249-0.0793-0.01690.0097-0.1053-0.02380.06680.0106-0.0143-0.00920.0101-0.0113-0.005-0.029923.060627.782236.7186
70.0420.03870.06460.0307-0.0070.15190.00680.006-0.03170.02120.01140.0117-0.03160.0105-0.0181-0.0068-0.00210.0243-0.0141-0.00630.00854.380521.33825.536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 24
2X-RAY DIFFRACTION2{ B|* }B2 - 24
3X-RAY DIFFRACTION3{ C|* }C2 - 24
4X-RAY DIFFRACTION4{ D|* }D2 - 24
5X-RAY DIFFRACTION5{ E|* }E2 - 24
6X-RAY DIFFRACTION6{ F|* }F2 - 24
7X-RAY DIFFRACTION7{ X|* }X1 - 12

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