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- PDB-1uwf: 1.7 A resolution structure of the receptor binding domain of the ... -

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Basic information

Entry
Database: PDB / ID: 1uwf
Title1.7 A resolution structure of the receptor binding domain of the FimH adhesin from uropathogenic E. coli
ComponentsFIMH PROTEIN
KeywordsCELL ADHESION / BACTERIAL ADHESIN / CARBOHYDRATE RECOGNITION / ADHERENCE TO MAMMALIAN CELLS / IG-VARIABLE FOLD
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
butyl alpha-D-mannopyranoside / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsBouckaert, J. / Berglund, J. / Genst, E.D. / Cools, L. / Hung, C.-S. / Wuhrer, M. / Zavialov, A. / Langermann, S. / Hultgren, S. / Wyns, L. ...Bouckaert, J. / Berglund, J. / Genst, E.D. / Cools, L. / Hung, C.-S. / Wuhrer, M. / Zavialov, A. / Langermann, S. / Hultgren, S. / Wyns, L. / Oscarson, S. / Knight, S.D. / De Greve, H.
CitationJournal: Mol.Microbiol. / Year: 2005
Title: Receptor Binding Studies Disclose a Novel Class of High-Affinity Inhibitors of the Escherichia Coli Fimh Adhesin.
Authors: Bouckaert, J. / Berglund, J. / Schembri, M. / De Genst, E. / Cools, L. / Wuhrer, M. / Hung, C. / Pinkner, J. / Slattegard, R. / Zavialov, A. / Choudhury, D. / Langermann, S. / Hultgren, S.J. ...Authors: Bouckaert, J. / Berglund, J. / Schembri, M. / De Genst, E. / Cools, L. / Wuhrer, M. / Hung, C. / Pinkner, J. / Slattegard, R. / Zavialov, A. / Choudhury, D. / Langermann, S. / Hultgren, S.J. / Wyns, L. / Klemm, P. / Oscarson, S. / Knight, S.D. / De Greve, H.
History
DepositionFeb 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2453
Polymers16,9171
Non-polymers3282
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.906, 41.636, 97.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FIMH PROTEIN / FIMH


Mass: 16916.828 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LECTIN DOMAIN, RESIDUES 22-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Plasmid: PMMB91 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600
Variant (production host): F-SUPE44 LACY1 THR-1 LEUB6 MCRB THI-1 FHUA21 HSDR LAMBDA
References: UniProt: P08191
#2: Sugar ChemComp-DEG / butyl alpha-D-mannopyranoside / BUTYL-A-D-MANNOSE / butyl alpha-D-mannoside / butyl D-mannoside / butyl mannoside


Type: D-saccharide / Mass: 236.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES 22-179 IN THE COMPND RECORD CORRESPOND TO RESIDUES 1-158 OF THE MATURE FIMH PROTEIN AND ...RESIDUES 22-179 IN THE COMPND RECORD CORRESPOND TO RESIDUES 1-158 OF THE MATURE FIMH PROTEIN AND THUS TO THE LECTIN DOMAIN OF THE ADHESIN.

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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: 2.34 Å3/Da / Density % sol: 38.5 % / Description: DATA WERE COLLECTED AT THE APS, CHICAGO, USA
Crystal growpH: 7.5
Details: 1.1 MM PROTEIN, 0.1 M HEPES PH 7.5, 10 % PEG6000, 5% V/V MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.488
DetectorDetector: CCD / Date: Dec 15, 2000
RadiationMonochromator: CARBON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.69→39 Å / Num. obs: 18597 / % possible obs: 98.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 27.25
Reflection shellResolution: 1.69→1.73 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 8.2 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QUN

1qun


Resolution: 1.69→38.27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1034321.06 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 1564 8.4 %RANDOM
Rwork0.1791 ---
obs0.1791 18545 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.7495 Å2 / ksol: 0.371833 e/Å3
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.49 Å20 Å20 Å2
2---1.44 Å20 Å2
3----4.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.69→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 22 307 1525
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.971.5
X-RAY DIFFRACTIONc_mcangle_it1.452
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.192.5
LS refinement shellResolution: 1.69→1.8 Å / Rfactor Rfree error: 0.137 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.454 11 0.4 %
Rwork0.257 2972 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GOL.PARGOL.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4DEG.PARDEG.TOP

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