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- PDB-4xo9: Crystal structure of a FimH*DsG complex from E.coli K12 in space ... -

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Basic information

Entry
Database: PDB / ID: 4xo9
TitleCrystal structure of a FimH*DsG complex from E.coli K12 in space group C2
Components
  • Minor component of type 1 fimbriae
  • Protein FimH
KeywordsCELL ADHESION / type I pilus / catch-bond / lectin / UPEC / bacterial adhesin / UTI / mannose / isomerase
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
: / Protein FimG / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsJakob, R.P. / Eras, J. / Glockshuber, R. / Maier, T.
CitationJournal: Nat Commun / Year: 2016
Title: Catch-bond mechanism of the bacterial adhesin FimH.
Authors: Sauer, M.M. / Jakob, R.P. / Eras, J. / Baday, S. / Eris, D. / Navarra, G. / Berneche, S. / Ernst, B. / Maier, T. / Glockshuber, R.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein FimH
B: Minor component of type 1 fimbriae


Theoretical massNumber of molelcules
Total (without water)30,4982
Polymers30,4982
Non-polymers00
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-11 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.490, 35.620, 72.890
Angle α, β, γ (deg.)90.00, 105.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-482-

HOH

21A-489-

HOH

31A-533-

HOH

41A-788-

HOH

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Components

#1: Protein Protein FimH


Mass: 29081.314 Da / Num. of mol.: 1 / Fragment: UNP residues 22-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P08191
#2: Protein/peptide Minor component of type 1 fimbriae


Mass: 1416.661 Da / Num. of mol.: 1 / Fragment: UNP residues 24-37
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / MC4100 / BW2952 / Gene: fimG, BWG_4017 / Plasmid: pTRC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: C4ZT07, UniProt: P08190*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25 % (w/v) polyethylene glycol (PEG) 3350, 0.2 M magnesium chloride, 0.1 M BisTris-HCl pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.14→45.784 Å / Num. obs: 85076 / % possible obs: 94.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.8
Reflection shellResolution: 1.14→1.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.8 / % possible all: 81.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1621)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mcy, 1qun

3mcy

1qun


Resolution: 1.14→45.784 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1432 2111 2.48 %
Rwork0.1247 --
obs0.1252 85076 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.14→45.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 0 533 2674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112223
X-RAY DIFFRACTIONf_angle_d1.4653065
X-RAY DIFFRACTIONf_dihedral_angle_d11.862769
X-RAY DIFFRACTIONf_chiral_restr0.089373
X-RAY DIFFRACTIONf_plane_restr0.008399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1401-1.16660.18651080.21134259X-RAY DIFFRACTION74
1.1666-1.19580.20711040.17925113X-RAY DIFFRACTION87
1.1958-1.22820.19121380.17135232X-RAY DIFFRACTION90
1.2282-1.26430.17881360.16365373X-RAY DIFFRACTION93
1.2643-1.30510.16921650.15415506X-RAY DIFFRACTION95
1.3051-1.35180.17631480.14525601X-RAY DIFFRACTION96
1.3518-1.40590.16711430.13295605X-RAY DIFFRACTION97
1.4059-1.46990.11211440.11425681X-RAY DIFFRACTION97
1.4699-1.54740.11981470.10815710X-RAY DIFFRACTION98
1.5474-1.64430.13111420.10635716X-RAY DIFFRACTION98
1.6443-1.77130.10311540.11025774X-RAY DIFFRACTION99
1.7713-1.94950.12841280.10885777X-RAY DIFFRACTION99
1.9495-2.23160.12371520.10445808X-RAY DIFFRACTION99
2.2316-2.81160.13931600.12415851X-RAY DIFFRACTION99
2.8116-45.82050.15711420.12665959X-RAY DIFFRACTION98

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