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- PDB-8bvd: FimH lectin domain in complex with mannose C-linked to quinoline -

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Basic information

Entry
Database: PDB / ID: 8bvd
TitleFimH lectin domain in complex with mannose C-linked to quinoline
ComponentsType 1 fimbrin D-mannose specific adhesin
KeywordsCELL ADHESION / Type-1 fimbriae / Escherichia coli / FimH / Adhesin / Lectin / Anti-adhesives / C-linked mannose
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
Chem-RLO / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli UTI89 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.995 Å
AuthorsBouckaert, J. / Bridot, C.
Funding support France, Canada, 2items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-05570 Canada
Citation
Journal: Pharmaceutics / Year: 2023
Title: Insightful Improvement in the Design of Potent Uropathogenic E. coli FimH Antagonists.
Authors: Mousavifar, L. / Sarshar, M. / Bridot, C. / Scribano, D. / Ambrosi, C. / Palamara, A.T. / Vergoten, G. / Roubinet, B. / Landemarre, L. / Bouckaert, J. / Roy, R.
#1: 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.
#2: 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 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _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
C: Type 1 fimbrin D-mannose specific adhesin
D: Type 1 fimbrin D-mannose specific adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9938
Polymers67,6674
Non-polymers1,3254
Water4,035224
1
A: Type 1 fimbrin D-mannose specific adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2482
Polymers16,9171
Non-polymers3311
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)17,2482
Polymers16,9171
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Type 1 fimbrin D-mannose specific adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2482
Polymers16,9171
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Type 1 fimbrin D-mannose specific adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2482
Polymers16,9171
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.784, 151.784, 225.034
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-322-

HOH

21B-382-

HOH

31C-328-

HOH

41D-316-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

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-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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


Mass: 16916.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli UTI89 (bacteria) / Strain: UTI89 / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P08191
#2: Chemical
ChemComp-RLO / (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-[(E)-3-quinolin-6-ylprop-2-enyl]oxane-3,4,5-triol / (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-((E)-3-(quinolin-6-yl)allyl)tetrahydro-2H-pyran-3,4,5-triol


Mass: 331.363 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H21NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 5.53 Å3/Da / Density % sol: 77.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 3.0M NaCl and 0.1M BIS-TRIS at pH=5.5 / PH range: 5.25 - 5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.995→49.732 Å / Num. obs: 31057 / % possible obs: 98.6 % / Redundancy: 39.4 % / CC1/2: 0.996 / Rrim(I) all: 0.464 / Net I/σ(I): 12.41
Reflection shellResolution: 3→3.18 Å / Redundancy: 40.2 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 4900 / CC1/2: 0.615 / Rrim(I) all: 3.422 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.995→49.732 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.83 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.206 / SU B: 17.437 / SU ML: 0.302 / Average fsc free: 0.9258 / Average fsc work: 0.9484 / Cross valid method: THROUGHOUT / ESU R: 0.669 / ESU R Free: 0.41
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3034 1439 4.974 %RANDOM
Rwork0.2512 27492 --
all0.254 ---
obs-28931 91.874 %-
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: 53.611 Å2
Baniso -1Baniso -2Baniso -3
1--0.117 Å2-0.059 Å2-0 Å2
2---0.117 Å20 Å2
3---0.381 Å2
Refinement stepCycle: LAST / Resolution: 2.995→49.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 96 224 5104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0115008
X-RAY DIFFRACTIONr_bond_other_d0.010.0164388
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.6696888
X-RAY DIFFRACTIONr_angle_other_deg0.5061.56810208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6655628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.735516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29110672
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.37710204
X-RAY DIFFRACTIONr_chiral_restr0.0580.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02996
X-RAY DIFFRACTIONr_nbd_refined0.1910.2929
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.24288
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22359
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.22730
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2204
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0910.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1180.223
X-RAY DIFFRACTIONr_nbd_other0.2510.2128
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.20.210
X-RAY DIFFRACTIONr_mcbond_it5.4975.8732524
X-RAY DIFFRACTIONr_mcbond_other5.4945.8732524
X-RAY DIFFRACTIONr_mcangle_it8.3528.7663148
X-RAY DIFFRACTIONr_mcangle_other8.358.7683149
X-RAY DIFFRACTIONr_scbond_it4.6985.8162484
X-RAY DIFFRACTIONr_scbond_other4.6975.8152485
X-RAY DIFFRACTIONr_scangle_it7.2648.653740
X-RAY DIFFRACTIONr_scangle_other7.2648.653741
X-RAY DIFFRACTIONr_lrange_it11.97269.5835355
X-RAY DIFFRACTIONr_lrange_other11.97169.5775356
X-RAY DIFFRACTIONr_ncsr_local_group_10.1450.054519
X-RAY DIFFRACTIONr_ncsr_local_group_20.1380.054639
X-RAY DIFFRACTIONr_ncsr_local_group_30.1190.054804
X-RAY DIFFRACTIONr_ncsr_local_group_40.140.054638
X-RAY DIFFRACTIONr_ncsr_local_group_50.150.054555
X-RAY DIFFRACTIONr_ncsr_local_group_60.1220.054739
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.144910.05008
12AX-RAY DIFFRACTIONLocal ncs0.144910.05008
23AX-RAY DIFFRACTIONLocal ncs0.137890.05009
24AX-RAY DIFFRACTIONLocal ncs0.137890.05009
35AX-RAY DIFFRACTIONLocal ncs0.118540.05009
36AX-RAY DIFFRACTIONLocal ncs0.118540.05009
47AX-RAY DIFFRACTIONLocal ncs0.139990.05009
48AX-RAY DIFFRACTIONLocal ncs0.139990.05009
59AX-RAY DIFFRACTIONLocal ncs0.150450.05008
510AX-RAY DIFFRACTIONLocal ncs0.150450.05008
611AX-RAY DIFFRACTIONLocal ncs0.122290.05009
612AX-RAY DIFFRACTIONLocal ncs0.122290.05009
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
2.995-3.0730.35340.3157560.31622550.9150.9335.03330.291
3.073-3.1570.415750.3414650.34422370.8940.91468.84220.317
3.157-3.2480.4691010.32519120.33121390.850.92394.10940.295
3.248-3.3480.3891050.28419920.2920990.8960.93999.90470.248
3.348-3.4570.4151000.34118950.34520450.8760.91597.5550.296
3.457-3.5770.362970.2918540.29319600.9190.94299.54080.256
3.577-3.7120.352920.3417370.34119160.9250.91995.45930.298
3.712-3.8620.317920.26717480.26918400.9260.9521000.233
3.862-4.0330.349820.30415830.30617670.9190.93894.22750.256
4.033-4.2290.25850.20216170.20517020.9560.9741000.174
4.229-4.4560.266810.19115440.19516250.9570.9761000.165
4.456-4.7230.235770.1914560.19315330.9670.9771000.165
4.723-5.0460.211730.18613830.18714560.9730.9781000.16
5.046-5.4460.206680.19612920.19713600.9740.9741000.171
5.446-5.9590.273630.21911920.22112550.9460.9661000.192
5.959-6.650.313580.23611040.2411620.9280.9611000.205
6.65-7.6560.264510.239790.23210300.960.9641000.202
7.656-9.3220.277450.238520.2328970.950.9651000.212
9.322-12.9570.281360.2246870.2277230.9420.9621000.208
12.957-49.7320.294240.2984440.2984680.9230.941000.279

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