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- PDB-6f7w: Crystal structure of dimethylated RSL - cucurbit[7]uril complex, ... -

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Basic information

Entry
Database: PDB / ID: 6f7w
TitleCrystal structure of dimethylated RSL - cucurbit[7]uril complex, C2221 Form
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / cucurbituril / dimethyllysine / supramolecular recognition
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: 1.28 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 / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_symmetry
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,77715
Polymers29,5283
Non-polymers4,24912
Water6,882382
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-28 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.343, 87.176, 146.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: Chemical ChemComp-QQ7 / cucurbit[7]uril


Mass: 1162.962 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 200 mM Sodium Malonate pH 7.0

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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: 1.28→43.6 Å / Num. obs: 78616 / % possible obs: 95 % / Redundancy: 4.5 % / CC1/2: 0.99 / Rpim(I) all: 0.022 / Rrim(I) all: 0.05 / Net I/σ(I): 18.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.28-1.341.937490.7060.380.50192.4
7.01-43.64.766.85000.9990.0140.03289.8

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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: 1.28→43.6 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.338 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0389 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.039
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1508 3865 4.9 %RANDOM
Rwork0.1236 ---
obs0.1249 74734 94.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.52 Å2 / Biso mean: 18.503 Å2 / Biso min: 9.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--1.05 Å20 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 1.28→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 301 385 2756
Biso mean--19.75 34.95 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0182530
X-RAY DIFFRACTIONr_bond_other_d0.0030.0192030
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.7383573
X-RAY DIFFRACTIONr_angle_other_deg1.01134733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6515273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49323.52388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.6215244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.735159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02492
X-RAY DIFFRACTIONr_rigid_bond_restr1.45534556
X-RAY DIFFRACTIONr_sphericity_free28.5735243
X-RAY DIFFRACTIONr_sphericity_bonded9.86554576
LS refinement shellResolution: 1.28→1.313 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 232 -
Rwork0.232 5419 -
all-5651 -
obs--93.4 %

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