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- PDB-7quo: FimH lectin domain in complex with oligomannose-6 -

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Basic information

Entry
Database: PDB / ID: 7quo
TitleFimH lectin domain in complex with oligomannose-6
ComponentsFimH
KeywordsCELL ADHESION / Type-1 fimbriae / Escherichia coli / FimH / Adhesin / Lectin / Oligomannose / High-mannose
Function / homology
Function and homology information


pilus / cell adhesion / metal ion binding
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / FimH
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBouckaert, J. / Bourenkov, G.P.
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. / 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
DepositionJan 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Feb 14, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FimH
B: FimH
C: FimH
D: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,88912
Polymers67,6674
Non-polymers3,2218
Water2,972165
1
A: FimH
C: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3485
Polymers33,8342
Non-polymers1,5153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FimH
D: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5407
Polymers33,8342
Non-polymers1,7075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.110, 153.110, 230.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
FimH


Mass: 16916.828 Da / Num. of mol.: 4 / Fragment: FIMH LECTIN DOMAIN, RESIDUES 22-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: fimH / Variant: C43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S497
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5.54 Å3/Da / Density meas: 0.3 Mg/m3 / Density % sol: 77.79 %
Description: small lentil-like crystals grown on a large salt beam
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1 M Lithium Sulfate 100 mM Tris-HCl, pH 8.5 10 mM Nickel Chloride 3% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 24, 2021 / Details: MD3 diffractometer
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3→230.41 Å / Num. obs: 59950 / % possible obs: 99.82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.93 % / Biso Wilson estimate: 64.52 Å2 / CC1/2: 0.902 / Rmerge(I) obs: 0.68 / Rrim(I) all: 0.67 / Net I/σ(I): 3.13
Reflection shellResolution: 3→3.08 Å / Redundancy: 5.82 % / Rmerge(I) obs: 4.97 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 25825 / CC1/2: 0.06 / Rrim(I) all: 5.25 / % possible all: 99.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FX3

5fx3


Resolution: 3→114.925 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.817 / SU ML: 0.45 / Cross valid method: FREE R-VALUE / ESU R: 0.301 / ESU R Free: 0.344 / Phase error: 25.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2756 1993 6.122 %Random selection
Rwork0.2358 30563 --
all0.241 ---
obs-32556 99.825 %-
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: 44.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.165 Å2-0 Å2
2---0.33 Å20 Å2
3---1.071 Å2
Refinement stepCycle: LAST / Resolution: 3→114.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 204 165 5153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0780.3581440.3472200X-RAY DIFFRACTION99.9147
3.078-3.1620.3681410.3342160X-RAY DIFFRACTION99.9566
3.162-3.2540.3381380.2932114X-RAY DIFFRACTION99.9556
3.254-3.3540.2951330.2892027X-RAY DIFFRACTION100
3.354-3.4640.291290.2741982X-RAY DIFFRACTION100
3.464-3.5850.3011280.2641942X-RAY DIFFRACTION99.8071
3.585-3.720.2791200.2511842X-RAY DIFFRACTION99.9491
3.72-3.8720.2471170.2361783X-RAY DIFFRACTION99.8424
3.872-4.0440.2421120.2191735X-RAY DIFFRACTION99.8918
4.044-4.2410.2781070.2061648X-RAY DIFFRACTION99.7726
4.241-4.470.2191030.1871575X-RAY DIFFRACTION99.7622
4.47-4.7410.225970.1791502X-RAY DIFFRACTION99.8127
4.741-5.0680.212930.1811410X-RAY DIFFRACTION99.8008
5.068-5.4730.233870.2081333X-RAY DIFFRACTION99.7892
5.473-5.9940.298800.2361210X-RAY DIFFRACTION99.768
5.994-6.6990.242730.2321120X-RAY DIFFRACTION99.8326
6.699-7.7310.288650.2131004X-RAY DIFFRACTION99.9065
7.731-9.4580.264550.189855X-RAY DIFFRACTION99.1285
9.458-13.3310.186440.193697X-RAY DIFFRACTION99.4631
13.331-114.9250.308270.271424X-RAY DIFFRACTION98.2571

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