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- PDB-6f7x: Crystal structure of dimethylated RSL - cucurbit[7]uril complex, ... -

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Basic information

Entry
Database: PDB / ID: 6f7x
TitleCrystal structure of dimethylated RSL - cucurbit[7]uril complex, F432 form
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / cucurbituril / dimethyllysine / supramolecular recognition
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
methyl alpha-L-fucopyranoside / cucurbit[7]uril / Fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.42 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 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.d_res_low
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Aug 5, 2020Group: Polymer sequence / Structure summary / Category: chem_comp / entity_poly
Item: _chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms ..._chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms / _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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,01512
Polymers29,5283
Non-polymers3,4879
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-2 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.550, 200.550, 200.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11C-252-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 2 - 90 / Label seq-ID: 2 - 90

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 9842.753 Da / Num. of mol.: 3 / 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: Sugar
ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside / Methyl group


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-QQ7 / cucurbit[7]uril


Mass: 1162.962 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H42N28O14
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350 100 mM Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.42→70.91 Å / Num. obs: 13677 / % possible obs: 99.8 % / Redundancy: 8.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.058 / Rrim(I) all: 0.175 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.42-2.518.60.53714160.8850.1920.572100
9.06-70.917.50.0543130.9730.0240.0696.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
Aimless0.5.27data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bt9 chain A

2bt9


Resolution: 2.42→70.91 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.1969 / WRfactor Rwork: 0.1487 / FOM work R set: 0.8491 / SU B: 7.454 / SU ML: 0.17 / SU R Cruickshank DPI: 0.4278 / SU Rfree: 0.2534 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.428 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 687 5 %RANDOM
Rwork0.1756 ---
obs0.1784 12981 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.91 Å2 / Biso mean: 15.836 Å2 / Biso min: 2.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.42→70.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 246 243 2577
Biso mean--32.53 16.02 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192445
X-RAY DIFFRACTIONr_bond_other_d0.0020.021980
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.8093428
X-RAY DIFFRACTIONr_angle_other_deg0.92234600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2585265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15423.44887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.25815241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.938159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02490
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A56140.06
12B56140.06
21A56120.08
22C56120.08
31B56340.07
32C56340.07
LS refinement shellResolution: 2.422→2.484 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 48 -
Rwork0.242 934 -
all-982 -
obs--100 %

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