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- PDB-4av4: FimH lectin domain co-crystal with a alpha-D-mannoside O-linked t... -

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Basic information

Entry
Database: PDB / ID: 4av4
TitleFimH lectin domain co-crystal with a alpha-D-mannoside O-linked to a propynyl pyridine
ComponentsFIMH
KeywordsCELL ADHESION / FIMBRIAE / VARIABLE IMMUNOGLOBULIN FOLD / URINARY TRACT INFECTION
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-FVQ / FimH / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBouckaert, J. / Touaibia, M. / Roos, G. / Shiao, T.C. / Wang, Q. / Papadopoulos, A. / Roy, R.
CitationJournal: Biochemistry / Year: 2012
Title: The Tyrosine Gate as a Potential Entropic Lever in the Receptor-Binding Site of the Bacterial Adhesin Fimh.
Authors: Wellens, A. / Lahmann, M. / Touaibia, M. / Vaucher, J. / Oscarson, S. / Roy, R. / Remaut, H. / Bouckaert, J.
History
DepositionMay 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Atomic model / Derived calculations / Other
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Jul 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 1.4Dec 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2112
Polymers16,9161
Non-polymers2951
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.470, 41.890, 95.050
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


Mass: 16915.842 Da / Num. of mol.: 1 / Fragment: LECTIN DOMAIN, RESIDUES 10-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: UTI89 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A2IC68, UniProt: P08191*PLUS
#2: Sugar ChemComp-FVQ / 3-(pyridin-3-yl)prop-2-yn-1-yl alpha-D-mannopyranoside / 3-pyridin-3-ylprop-2-yn-1-yl alpha-D-mannopyranoside / D-MANNOSE ALPHA1O-PROPYNYL PYRIDINE / 3-(pyridin-3-yl)prop-2-yn-1-yl alpha-D-mannoside / 3-(pyridin-3-yl)prop-2-yn-1-yl D-mannoside / 3-(pyridin-3-yl)prop-2-yn-1-yl mannoside


Type: D-saccharide / Mass: 295.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17NO6
#3: Water ChemComp-HOH / water


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

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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: 1.86 Å3/Da / Density % sol: 33.86 % / Description: NONE
Crystal growpH: 8.6
Details: 30 % (V/V) 2-PROPANOL, 100 MM TRIS-HCL PH 8.5, 200 MM AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0
ReflectionResolution: 1.9→38.3 Å / Num. obs: 11106 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 21.01 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.23
Reflection shellResolution: 1.9→2.09 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.18 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VCO

2vco


Resolution: 1.9→38.332 Å / SU ML: 0.24 / σ(F): 2 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 554 5 %
Rwork0.1776 --
obs0.181 11072 99.97 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.688 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0251 Å20 Å20 Å2
2---0.4577 Å20 Å2
3----0.5674 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 21 165 1382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161274
X-RAY DIFFRACTIONf_angle_d1.6211758
X-RAY DIFFRACTIONf_dihedral_angle_d19.415454
X-RAY DIFFRACTIONf_chiral_restr0.091209
X-RAY DIFFRACTIONf_plane_restr0.008227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.09120.33321350.24822580X-RAY DIFFRACTION100
2.0912-2.39380.27091350.18932571X-RAY DIFFRACTION100
2.3938-3.01570.28151380.16942619X-RAY DIFFRACTION100
3.0157-38.34020.19251460.162748X-RAY DIFFRACTION100

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