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- PDB-5o7w: Crystal structure of the 4-FLUORO RSL lectin in complex with Lewi... -

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Basic information

Entry
Database: PDB / ID: 5o7w
TitleCrystal structure of the 4-FLUORO RSL lectin in complex with Lewis x tetrasaccharide
ComponentsPutative fucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / lectin / fluorinated tryptophan / lewis X / CARBOHYDRATE
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
Fucose-binding lectin protein / Putative fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsVarrot, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-SYNB-0002 France
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Effect of Noncanonical Amino Acids on Protein-Carbohydrate Interactions: Structure, Dynamics, and Carbohydrate Affinity of a Lectin Engineered with Fluorinated Tryptophan Analogs.
Authors: Tobola, F. / Lelimousin, M. / Varrot, A. / Gillon, E. / Darnhofer, B. / Blixt, O. / Birner-Gruenberger, R. / Imberty, A. / Wiltschi, B.
History
DepositionJun 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative fucose-binding lectin protein
B: Putative fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5727
Polymers19,7192
Non-polymers1,8535
Water5,206289
1
A: Putative fucose-binding lectin protein
hetero molecules

A: Putative fucose-binding lectin protein
hetero molecules

A: Putative fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7559
Polymers29,5783
Non-polymers3,1776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation23_555y,-z+1/2,-x+1/21
crystal symmetry operation32_555-z+1/2,x,-y+1/21
Buried area10190 Å2
ΔGint46 kcal/mol
Surface area11680 Å2
MethodPISA
2
B: Putative fucose-binding lectin protein
hetero molecules

B: Putative fucose-binding lectin protein
hetero molecules

B: Putative fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,96012
Polymers29,5783
Non-polymers2,3819
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_554-z,-x+1/2,y-1/21
crystal symmetry operation46_555-y+1/2,z+1/2,-x1
Buried area8550 Å2
ΔGint41 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.465, 130.465, 130.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

21A-279-

HOH

31A-300-

HOH

41A-303-

HOH

51A-326-

HOH

61B-209-

HOH

71B-306-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative fucose-binding lectin protein


Mass: 9859.499 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ALL TRYTOPHANE ARE 4-FLUORINATED / Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: CMR15_11270 / Plasmid: pQE80L-RSL / Production host: Escherichia coli (E. coli) / Strain (production host): BWEC47 / References: UniProt: D8NA05, UniProt: A0A0S4TLR1*PLUS

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 691.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAcb1-3DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2112h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3-4/a3-b1_b3-c1_b4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 691.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-1/a3-b1_b3-c1_b4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 291 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.39 Å3/Da / Density % sol: 48.47 % / Description: BIPYRAMIDAL
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Morpheus 1-9: 60mM divalent, 100 mM buffer pH 7.5, 20% peg550MME and 10M peg20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.93221 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93221 Å / Relative weight: 1
ReflectionResolution: 1.35→19.9 Å / Num. obs: 40182 / % possible obs: 99.5 % / Redundancy: 6.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.023 / Net I/σ(I): 22.6
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 8.7 / Num. unique obs: 1980 / CC1/2: 0.984 / Rpim(I) all: 0.074 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDS20160617data reduction
Aimless0.5.31data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5o7V

5o7v


Resolution: 1.35→19.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.303 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.048 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15573 2052 5.1 %RANDOM
Rwork0.12654 ---
obs0.12799 38130 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 6.173 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.35→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 125 289 1792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021645
X-RAY DIFFRACTIONr_bond_other_d0.0030.021342
X-RAY DIFFRACTIONr_angle_refined_deg1.8032.1762289
X-RAY DIFFRACTIONr_angle_other_deg0.9533143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg29.95.92201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63324.63441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26115179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.469156
X-RAY DIFFRACTIONr_chiral_restr0.1070.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6060.368740
X-RAY DIFFRACTIONr_mcbond_other0.6060.368739
X-RAY DIFFRACTIONr_mcangle_it0.7720.552932
X-RAY DIFFRACTIONr_mcangle_other0.7720.552933
X-RAY DIFFRACTIONr_scbond_it0.8760.549905
X-RAY DIFFRACTIONr_scbond_other0.8750.549905
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.010.7641358
X-RAY DIFFRACTIONr_long_range_B_refined2.1956.2181924
X-RAY DIFFRACTIONr_long_range_B_other1.6725.3411856
X-RAY DIFFRACTIONr_rigid_bond_restr1.96132987
X-RAY DIFFRACTIONr_sphericity_free20.8775191
X-RAY DIFFRACTIONr_sphericity_bonded4.4953044
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 141 -
Rwork0.181 2792 -
obs--98.13 %

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