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- PDB-4xod: Crystal structure of a FimH*DsG complex from E.coli F18 -

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Basic information

Entry
Database: PDB / ID: 4xod
TitleCrystal structure of a FimH*DsG complex from E.coli F18
Components
  • FimG protein
  • FimH protein
KeywordsCELL ADHESION / type I pilus / catch-bond / lectin / UPEC / bacterial adhesin / UTI / 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
Protein FimG / Type 1 fimbrin D-mannose specific adhesin / FimH protein / FimG protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsJakob, R.P. / Sauer, M.M. / 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 / 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
Revision 1.3Oct 16, 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
B: FimG protein
A: FimH protein


Theoretical massNumber of molelcules
Total (without water)30,4702
Polymers30,4702
Non-polymers00
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-11 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.310, 35.540, 72.790
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-483-

HOH

21A-496-

HOH

31A-531-

HOH

41A-580-

HOH

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Components

#1: Protein/peptide FimG protein


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 (E. coli) / Gene: ECP_4654 / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: Q0T8Y9, UniProt: P08190*PLUS
#2: Protein FimH protein


Mass: 29053.260 Da / Num. of mol.: 1 / Fragment: UNP residues 25-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECP_4655 / Plasmid: pTRC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: Q0T8Y8, UniProt: P08191*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.03 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25 % (w/v) 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: X06DA / Wavelength: 0.99999 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: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.14→47.779 Å / Num. obs: 87277 / % possible obs: 97.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 16.6
Reflection shellResolution: 1.14→1.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.6 / Num. unique all: 12781 / % possible all: 88

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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→47.779 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 15.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1585 2172 2.49 %
Rwork0.1424 --
obs0.1428 87277 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.14→47.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 0 552 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062248
X-RAY DIFFRACTIONf_angle_d1.1663108
X-RAY DIFFRACTIONf_dihedral_angle_d11.409783
X-RAY DIFFRACTIONf_chiral_restr0.065380
X-RAY DIFFRACTIONf_plane_restr0.005404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1398-1.16460.29351090.26774239X-RAY DIFFRACTION79
1.1646-1.19170.26181090.25415043X-RAY DIFFRACTION92
1.1917-1.22150.23171320.23135202X-RAY DIFFRACTION96
1.2215-1.25450.24581320.22125287X-RAY DIFFRACTION98
1.2545-1.29140.21071540.20685324X-RAY DIFFRACTION99
1.2914-1.33310.20071490.1945369X-RAY DIFFRACTION100
1.3331-1.38070.21831450.17495441X-RAY DIFFRACTION100
1.3807-1.4360.15771240.15745418X-RAY DIFFRACTION100
1.436-1.50140.14421470.13695449X-RAY DIFFRACTION100
1.5014-1.58060.1411360.12455405X-RAY DIFFRACTION100
1.5806-1.67960.1411480.12245435X-RAY DIFFRACTION100
1.6796-1.80930.12651330.12515455X-RAY DIFFRACTION100
1.8093-1.99140.13041210.125472X-RAY DIFFRACTION100
1.9914-2.27950.1431530.11775466X-RAY DIFFRACTION100
2.2795-2.87190.1381470.1355483X-RAY DIFFRACTION100
2.8719-47.82090.16091330.1315617X-RAY DIFFRACTION99

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