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- PDB-6f7y: Crystal structure of dimethylated RSL, cucurbituril-free form -

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Basic information

Entry
Database: PDB / ID: 6f7y
TitleCrystal structure of dimethylated RSL, cucurbituril-free form
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / dimethyllysine
Function / homologyLipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / carbohydrate binding / Beta Barrel / Mainly Beta / metal ion binding / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsGuagnini, F. / Rennie, M.L. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/ERC/B2912 and 13/CDA/2168 Ireland
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein.
Authors: Guagnini, F. / Antonik, P.M. / Rennie, M.L. / O'Byrne, P. / Khan, A.R. / Pinalli, R. / Dalcanale, E. / Crowley, P.B.
History
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Aug 5, 2020Group: Data collection / Polymer sequence / Category: chem_comp / entity_poly
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 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
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
D: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,20013
Polymers39,3714
Non-polymers8299
Water5,657314
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)30,35712
Polymers29,5283
Non-polymers8299
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 area6790 Å2
ΔGint-19 kcal/mol
Surface area12480 Å2
MethodPISA
2
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
D: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0819
Polymers29,5283
Non-polymers5536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-22 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.285, 122.285, 36.418
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

21A-274-

HOH

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Components

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


Mass: 9842.753 Da / Num. of mol.: 4 / Mutation: S88A
Source method: isolated from a genetically manipulated source
Details: Recombinant protein dimethylated at lysine residues and N-terminus
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: RSP795_21825, RSP799_05830, RUN39_v1_50103 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 200 mM Potassium Formate pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→40.03 Å / Num. obs: 41544 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rpim(I) all: 0.047 / Rrim(I) all: 0.124 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.626.21.219380.4170.6371.67895.9
8.75-40.036.544.52770.9980.0180.04797.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bt9 chain A

2bt9


Resolution: 1.6→40.03 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.142 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0942 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.092
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 2114 5.1 %RANDOM
Rwork0.1689 ---
obs0.1704 39390 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.38 Å2 / Biso mean: 21.471 Å2 / Biso min: 7.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.6→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 54 320 3134
Biso mean--24.49 32.01 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022905
X-RAY DIFFRACTIONr_bond_other_d0.0020.022460
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.93978
X-RAY DIFFRACTIONr_angle_other_deg0.84535671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8735356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04823.559118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.44715323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.9091512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02655
LS refinement shellResolution: 1.6→1.638 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 123 -
Rwork0.305 2805 -
all-2928 -
obs--96.41 %

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