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- PDB-8bxy: FimH in complex with alpha1,6 core-fucosylated oligomannose-3, cr... -

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Basic information

Entry
Database: PDB / ID: 8bxy
TitleFimH in complex with alpha1,6 core-fucosylated oligomannose-3, crystallized in the trigonal space group
ComponentsType 1 fimbrin D-mannose specific adhesin
KeywordsCELL ADHESION / adhesin / FimH / core fucose
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBridot, C. / Bouckaert, J. / Krammer, E.-M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission750280European Union
Citation
Journal: J.Biol.Chem. / Year: 2023
Title: Structural insights into a cooperative switch between one and two FimH bacterial adhesins binding pauci- and high-mannose type N-glycan receptors.
Authors: Krammer, E.M. / Bridot, C. / Serna, S. / Echeverria, B. / Semwal, S. / Roubinet, B. / van Noort, K. / Wilbers, R.H.P. / Bourenkov, G. / de Ruyck, J. / Landemarre, L. / Reichardt, N. / Bouckaert, J.
#1: Journal: PLoS One / Year: 2008
Title: Intervening with urinary tract infections using anti-adhesives based on the crystal structure of the FimH-oligomannose-3 complex.
Authors: Wellens, A. / Garofalo, C. / Nguyen, H. / Van Gerven, N. / Slattegard, R. / Hernalsteens, J.P. / Wyns, L. / Oscarson, S. / De Greve, H. / Hultgren, S. / Bouckaert, J.
#2: Journal: Molecules / Year: 2017
Title: Sites for Dynamic Protein-Carbohydrate Interactions of O- and C-Linked Mannosides on the E. coli FimH Adhesin.
Authors: Touaibia, M. / Krammer, E.M. / Shiao, T.C. / Yamakawa, N. / Wang, Q. / Glinschert, A. / Papadopoulos, A. / Mousavifar, L. / Maes, E. / Oscarson, S. / Vergoten, G. / Lensink, M.F. / Roy, R. / Bouckaert, J.
#3: Journal: Molecules / Year: 2018
Title: A Novel Integrated Way for Deciphering the Glycan Code for the FimH Lectin.
Authors: Dumych, T. / Bridot, C. / Gouin, S.G. / Lensink, M.F. / Paryzhak, S. / Szunerits, S. / Blossey, R. / Bilyy, R. / Bouckaert, J. / Krammer, E.M.
History
DepositionDec 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 26, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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: Type 1 fimbrin D-mannose specific adhesin
B: Type 1 fimbrin D-mannose specific adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1617
Polymers33,8342
Non-polymers2,3275
Water6,215345
1
A: Type 1 fimbrin D-mannose specific adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1294
Polymers16,9171
Non-polymers1,2123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type 1 fimbrin D-mannose specific adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0323
Polymers16,9171
Non-polymers1,1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.056, 91.056, 79.578
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 158 / Label seq-ID: 1 - 158

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Type 1 fimbrin D-mannose specific adhesin / Protein FimH


Mass: 16916.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08191
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.66 % / Description: diamond-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1.1 M Lithium sulphate; 0.1 M Tris-HCl pH 9.0; 10 mM nickel chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.45→56.076 Å / Num. obs: 56199 / % possible obs: 95.16 % / Redundancy: 20.11 % / Biso Wilson estimate: 24.99 Å2 / CC1/2: 0.9996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.017 / Rrim(I) all: 0.077 / Net I/σ(I): 19.325
Reflection shellResolution: 1.45→1.556 Å / Redundancy: 16.95 % / Rmerge(I) obs: 1.837 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2811 / CC1/2: 0.615 / Rpim(I) all: 0.639 / Rrim(I) all: 1.949 / % possible all: 21.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PHENIX1.19.2_4158refinement
PHENIX1.17.1_3660model building
autoPROCdata processing
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→56.076 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.074
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2054 1481 2.635 %
Rwork0.1532 54717 -
all0.155 --
obs-56198 82.867 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.691 Å2
Baniso -1Baniso -2Baniso -3
1-0.603 Å20.301 Å2-0 Å2
2--0.603 Å20 Å2
3----1.955 Å2
Refinement stepCycle: LAST / Resolution: 1.45→56.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 151 345 2888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0122630
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.6663632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0845318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.98458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96210338
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.43210102
X-RAY DIFFRACTIONr_chiral_restr0.4370.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021928
X-RAY DIFFRACTIONr_nbd_refined0.1960.21127
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21832
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2256
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.229
X-RAY DIFFRACTIONr_mcbond_it5.0912.6581272
X-RAY DIFFRACTIONr_mcangle_it5.5843.9861590
X-RAY DIFFRACTIONr_scbond_it16.3443.521358
X-RAY DIFFRACTIONr_scangle_it13.6325.1172042
X-RAY DIFFRACTIONr_lrange_it10.16653.7654062
X-RAY DIFFRACTIONr_rigid_bond_restr23.86332630
X-RAY DIFFRACTIONr_ncsr_local_group_10.1130.054780
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.112880.05008
12AX-RAY DIFFRACTIONLocal ncs0.112880.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.45-1.4870.327140.33510.30149410.9250.9527.38720.296
1.487-1.5280.33320.28211870.28348700.9330.95925.03080.276
1.528-1.5720.328530.26721580.26846930.9310.96647.11270.254
1.572-1.6210.3281020.25237690.25445600.9220.9784.89040.234
1.621-1.6740.2861160.23242730.23444270.9360.97599.14160.213
1.674-1.7320.2741150.20841530.2143150.9580.97898.91080.185
1.732-1.7980.2381090.17440190.17641490.9640.98499.49390.154
1.798-1.8710.1721050.1438460.1439830.9830.98999.19660.124
1.871-1.9540.2161000.11937160.12138400.9720.99299.3750.109
1.954-2.0490.242970.12935800.13236950.9670.99199.51290.123
2.049-2.160.186920.13433980.13535010.9820.99199.68580.128
2.16-2.2910.206850.13432250.13633160.9750.99199.81910.129
2.291-2.4490.207780.14130200.14231030.9750.98899.83890.134
2.449-2.6450.191790.14328390.14529190.9790.98899.96570.138
2.645-2.8960.231690.15626200.15826900.9710.98699.96280.153
2.896-3.2370.179630.15923790.1624420.9770.9851000.16
3.237-3.7360.194580.15421130.15521710.9750.9861000.158
3.736-4.5710.173510.1218090.12218600.9820.9911000.13
4.571-6.4420.161370.14814220.14814590.9890.991000.159
6.442-56.0760.257260.2128410.2138670.9610.9621000.223

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