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- PDB-6zuk: Crystal structure of dimethylated RSL-N23H/G68H (RSL-B6) in compl... -

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Basic information

Entry
Database: PDB / ID: 6zuk
TitleCrystal structure of dimethylated RSL-N23H/G68H (RSL-B6) in complex with cucurbit[7]uril and zinc
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / cucurbituril / molecular glue / crystal engineering / dimethyllysine / zinc / b-propeller
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
cucurbit[7]uril / Fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsGuagnini, F. / Engilberge, S. / Flood, R.J. / Ramberg, K.O. / Crowley, P.B.
Funding support Ireland, 3items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation Ireland12/RC/2275_P2 Ireland
Irish Research CouncilGOIPD/2019/513 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2020
Title: Metal-Mediated Protein-Cucurbituril Crystalline Architectures
Authors: Guagnini, F. / Engilberge, S. / Flood, R.J. / Ramberg, K.O. / Crowley, P.B.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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)65,46928
Polymers58,3186
Non-polymers7,15122
Water5,459303
1
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,55118
Polymers29,1593
Non-polymers4,39115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-100 kcal/mol
Surface area13730 Å2
MethodPISA
2
D: Fucose-binding lectin protein
E: Fucose-binding lectin protein
F: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,91910
Polymers29,1593
Non-polymers2,7607
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-91 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.482, 50.631, 74.807
Angle α, β, γ (deg.)71.120, 83.150, 60.130
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 9719.712 Da / Num. of mol.: 6 / Mutation: N23H, H60S, T67N, G68H, T69G, T70K
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

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Non-polymers , 5 types, 325 molecules

#2: Chemical
ChemComp-QQ7 / cucurbit[7]uril


Mass: 1162.962 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C42H42N28O14 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#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.: 303 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3% PEG 8000, 0.1 M BIS-TRIS-HCl pH 7.0, 0.1 M magnesium chloride

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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 EIGER2 X 9M / Detector: PIXEL / Date: Jan 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 2.028→43.72 Å / Num. obs: 38198 / % possible obs: 97.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 34 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.067 / Rrim(I) all: 0.126 / Net I/σ(I): 7.3
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
2.03-2.143.70.4632039755160.8760.280.5422.496.9
6.41-43.723.60.07445212200.9880.0440.08315.198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.03 Å43.72 Å
Translation2.03 Å43.72 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (29-NOV-2019)refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F7W polyalanine

6f7w


Resolution: 2.03→43.72 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.185
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 1741 4.56 %RANDOM
Rwork0.2195 ---
obs0.2212 38179 97.1 %-
Displacement parametersBiso max: 104.71 Å2 / Biso mean: 37.19 Å2 / Biso min: 8.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.3016 Å20.9323 Å20.2286 Å2
2---3.0709 Å2-1.7937 Å2
3---2.7693 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.03→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 3237 303 7644
Biso mean--37.5 38.26 -
Num. residues----216
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1681SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes981HARMONIC24
X-RAY DIFFRACTIONt_it4808HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion555SEMIHARMONIC5
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_contact3499SEMIHARMONIC24
X-RAY DIFFRACTIONt_bond_d5098HARMONIC240.004
X-RAY DIFFRACTIONt_angle_deg7488HARMONIC240.49
X-RAY DIFFRACTIONt_omega_torsion4.76
X-RAY DIFFRACTIONt_other_torsion15.79
LS refinement shellResolution: 2.03→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2893 32 4.19 %
Rwork0.2099 732 -
all0.2133 764 -
obs--96.86 %

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