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- PDB-6yhw: Co-crystals in the P212121 space group, of a beta-cyclodextrin sp... -

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Basic information

Entry
Database: PDB / ID: 6yhw
TitleCo-crystals in the P212121 space group, of a beta-cyclodextrin spacered by triazole heptyl from alpha-D-mannose, with FimH lectin at 2.00 A resolution.
ComponentsFimH
KeywordsCELL ADHESION / beta-cyclodextrin host-guest interactions inhibitor design
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like ...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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-cyclodextrin / HEPTANE / alpha-D-mannopyranose / 2H-1,2,3-TRIAZOL-4-YLMETHANOL / Type 1 fimbrin D-mannose specific adhesin / FimH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.962 Å
Authorsde Ruyck, J. / Bouckaert, J.
Citation
Journal: Chembiochem / Year: 2016
Title: The Antiadhesive Strategy in Crohn's Disease: Orally Active Mannosides to Decolonize Pathogenic Escherichia coli from the Gut.
Authors: Alvarez Dorta, D. / Sivignon, A. / Chalopin, T. / Dumych, T.I. / Roos, G. / Bilyy, R.O. / Deniaud, D. / Krammer, E.M. / de Ruyck, J. / Lensink, M.F. / Bouckaert, J. / Barnich, N. / Gouin, S.G.
#1: Journal: Chemistry / Year: 2013
Title: Heptyl a-D-mannosides grafted on a b-cyclodextrin core to interfere with Escherichia coli adhesion: an in vivo multivalent effect.
Authors: Bouckaert, J. / Li, Z. / Xavier, C. / Almant, M. / Caveliers, V. / Lahoutte, T. / Weeks, S.D. / Kovensky, J. / Gouin, S.G.
#2: Journal: Chembiochem / Year: 2016
Title: The Antiadhesive Strategy in Crohn's Disease: Orally Active Mannosides to Decolonize Pathogenic Escherichia coli from the Gut.
Authors: Alvarez Dorta, D. / Sivignon, A. / Chalopin, T. / Dumych, T.I. / Roos, G. / Bilyy, R.O. / Deniaud, D. / Krammer, E.M. / de Ruyck, J. / Lensink, M.F. / Bouckaert, J. / Barnich, N. / Gouin, S.G.
#3: Journal: Molecules / Year: 2018
Title: Targeting Dynamical Binding Processes in the Design of Non-Antibiotic Anti-Adhesives by Molecular Simulation-The Example of FimH.
Authors: Krammer, E.M. / de Ruyck, J. / Roos, G. / Bouckaert, J. / Lensink, M.F.
#4: Journal: Expert Opin Ther Targets / Year: 2017
Title: The potential of FimH as a novel therapeutic target for the treatment of Crohn's disease.
Authors: Sivignon, A. / Bouckaert, J. / Bernard, J. / Gouin, S.G. / Barnich, N.
#5: Book title: Biophysical Techniques in Drug Discovery / Journal: Biophysical Techniques in Drug Discovery / Year: 2018
Title: Chapter 4 Molecular Mechanisms of Drug Action: X-ray Crystallography at the Basis of Structure-based and Ligand-based Drug Design
Authors: de Ruyck, J. / Roos, G. / Krammer, E.-M. / Prevost, M. / Lensink, M.F. / Bouckaert, J.
History
DepositionMar 31, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionMay 6, 2020ID: 5AB1
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / pdbx_validate_symm_contact / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Jan 24, 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: FimH
B: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,04110
Polymers62,9772
Non-polymers3,0658
Water6,305350
1
A: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0215
Polymers31,4881
Non-polymers1,5324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0215
Polymers31,4881
Non-polymers1,5324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.282, 68.072, 95.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FimH / FimH protein / Fimbrial protein / Minor component of type 1 fimbriae / Minor fimbrial subunit / D- ...FimH protein / Fimbrial protein / Minor component of type 1 fimbriae / Minor fimbrial subunit / D-mannose specific adhesin / Protein FimH / S-fimbrial protein subunit SfaH / Type 1 fimbria D-mannose specific adhesin FimH / Type 1 fimbrial adhesin


Mass: 31488.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: fimH, fimH_1, fimH_2, fimH_3, sfaH_2, A6581_19835, ACN81_00940, AKG99_10920, AM446_24165, AM464_16260, AUQ13_11280, AWG78_008695, B6V57_25500, B9M99_24715, B9T59_08965, BON65_08035, BON69_ ...Gene: fimH, fimH_1, fimH_2, fimH_3, sfaH_2, A6581_19835, ACN81_00940, AKG99_10920, AM446_24165, AM464_16260, AUQ13_11280, AWG78_008695, B6V57_25500, B9M99_24715, B9T59_08965, BON65_08035, BON69_13145, BON76_10045, BON87_19590, BvCms12BK_05011, BvCms2454_04206, C2U48_10910, C5P44_07835, C6B13_05760, CR538_22045, CRX46_08755, D2188_19245, D9G11_20470, D9H70_11375, D9I97_23340, D9J60_03345, DJ503_16470, DNQ45_27015, DS732_03965, DU321_25405, DXT73_23425, E0L12_19135, EC3234A_192c00060, ECONIH1_25860, ECTO6_04155, EIA21_01475, ELV08_23920, EQ830_16720, ERS085383_04267, F0312_06085, F1E19_12715, FNJ69_21090, FNJ83_00985, FV293_11400, FY127_19655, MS6198_50840, MS8345_04977, NCTC10090_02366, NCTC8450_00821, NCTC9045_05036, SAMEA3472056_01232, YDC107_3079
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q6JKW3, UniProt: P08191*PLUS

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Sugars , 2 types, 4 molecules

#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 354 molecules

#3: Chemical ChemComp-TA5 / 2H-1,2,3-TRIAZOL-4-YLMETHANOL


Mass: 99.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.64 Å3/Da / Density % sol: 24.9 % / Description: large bars
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: FimH (10 mg/mL) with beta-cyclodextrin triazole heptyl a-d-mannose (2 mM). Crystals were equilibrated against a well containing sodium citrate tribasic dihydrate buffer (pH 6.5, 1.6M). Prior ...Details: FimH (10 mg/mL) with beta-cyclodextrin triazole heptyl a-d-mannose (2 mM). Crystals were equilibrated against a well containing sodium citrate tribasic dihydrate buffer (pH 6.5, 1.6M). Prior to data collection, crystals were cryoprotected with use of reservoir solution containing glycerol (20%) and flash-cooled in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2015
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.962→48.348 Å / Num. obs: 29988 / % possible obs: 98.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 21.38 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6
Reflection shellResolution: 1.962→2.161 Å / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7379 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UWF

1uwf


Resolution: 1.962→46.348 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 1514 5.1 %random
Rwork0.2124 ---
obs0.2151 26630 98.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.12 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.962→46.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 204 350 2946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632684
X-RAY DIFFRACTIONf_angle_d0.8613710
X-RAY DIFFRACTIONf_chiral_restr0.0516478
X-RAY DIFFRACTIONf_plane_restr0.0055444
X-RAY DIFFRACTIONf_dihedral_angle_d10.85781008
LS refinement shellResolution: 1.962→2.025 Å
RfactorNum. reflection% reflection
Rfree0.3462 --
Rwork0.2991 2498 -
obs--97 %

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