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

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Basic information

Entry
Database: PDB / ID: 4xoe
TitleCrystal structure of a FimH*DsG complex from E.coli F18 with bound heptyl alpha-D-mannopyrannoside
Components
  • FimG protein
  • FimH protein
KeywordsCELL ADHESION / type I pilus / catch-bond / lectin / UPEC / bacterial adhesion / UTI / mannose / isomerase
Function / homology
Function and homology information


pilus / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / FimG protein / FimH protein / FimH protein / FimG protein
Similarity search - Component
Biological speciesEscherichia coli O6:K15:H31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJakob, R.P. / Sauer, M.M. / Navarra, G. / Ernst, B. / 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 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: FimH protein
B: FimG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8854
Polymers30,4702
Non-polymers4152
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-7 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.360, 128.360, 128.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-588-

HOH

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Components

#1: 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 O6:K15:H31 (bacteria) / Strain: F18 / Gene: ECP_4655 / Plasmid: pTRC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: Q0T8Y8, UniProt: A0A454AB91*PLUS
#2: 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 O6:K15:H31 (bacteria) / Strain: F18 / Gene: ECP_4654 / Plasmid: pTRC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: Q0T8Y9, UniProt: A0A140UH97*PLUS
#3: Sugar ChemComp-KGM / heptyl alpha-D-mannopyranoside / Heptyl Alpha-D-mannopyrannoside / heptyl alpha-D-mannoside / heptyl D-mannoside / heptyl mannoside


Type: D-saccharide / Mass: 278.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26O6 / Comment: detergent*YM
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 % (v/v) 2-Methyl-2,4-pentanediol (MPD), 0.1 M sodium cacodylate, 0.2 M magnesium acetate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97928 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.4→57.404 Å / Num. obs: 27814 / % possible obs: 99.9 % / Redundancy: 20 % / Rmerge(I) obs: 0.207 / Net I/σ(I): 18.3
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 20 % / Rmerge(I) obs: 2.024 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2605 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1779)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mcy, 1qun

3mcy

1qun


Resolution: 2.4→57.404 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1788 1393 5.01 %Random selection
Rwork0.1508 ---
obs0.1522 27814 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→57.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 24 323 2495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042227
X-RAY DIFFRACTIONf_angle_d0.8823055
X-RAY DIFFRACTIONf_dihedral_angle_d12.278759
X-RAY DIFFRACTIONf_chiral_restr0.033371
X-RAY DIFFRACTIONf_plane_restr0.004393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.4860.27961380.25262590X-RAY DIFFRACTION100
2.486-2.58550.29561360.22882655X-RAY DIFFRACTION100
2.5855-2.70320.21141340.20242583X-RAY DIFFRACTION100
2.7032-2.84570.21831380.18122632X-RAY DIFFRACTION100
2.8457-3.0240.18481370.16652633X-RAY DIFFRACTION100
3.024-3.25740.1871360.14832625X-RAY DIFFRACTION100
3.2574-3.58520.16911410.13492640X-RAY DIFFRACTION100
3.5852-4.10390.19451380.13332639X-RAY DIFFRACTION100
4.1039-5.16990.11731450.11472670X-RAY DIFFRACTION100
5.1699-57.42070.17251500.14532754X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.20222.28760.1046.06372.16362.01950.01250.39820.8181-1.16280.12310.1879-0.5901-0.0325-0.17670.47540.0340.09250.2910.09210.341-5.3507-45.0055-3.2649
20.6159-0.5821-0.49174.01784.24934.52380.02610.0050.4515-0.3088-0.1186-0.0094-0.3686-0.17770.14420.45020.00750.01830.23960.00530.3863-8.699-37.312710.2125
32.58361.45922.02654.11543.30024.05640.1336-0.18230.18680.2549-0.0785-0.04640.009-0.1738-0.04070.31680.04130.05320.24380.02020.2375-9.7515-50.058710.9272
40.6847-0.2157-0.26482.80242.22812.82410.10780.04170.2547-0.15130.0462-0.1842-0.37050.0356-0.12210.34470.01630.03330.19570.0210.2651-6.2661-45.28418.5546
50.6761-0.22340.19493.01891.92421.5949-0.04290.1032-0.0256-1.0293-0.1475-0.3162-0.583-0.02990.09820.6013-0.00290.07220.2634-0.0550.3909-4.4624-16.562324.9076
61.4246-0.26020.39413.16761.8932.4944-0.07270.0138-0.0891-0.3029-0.27830.22450.0153-0.18090.32230.37280.02020.00030.2639-0.07010.3877-11.0755-20.698933.1889
76.258-0.1069-1.07856.6259-0.50946.03620.04530.1043-0.139-0.22890.0293-0.5672-0.12840.6539-0.01850.3358-0.0429-0.01970.2827-0.09110.30621.7146-8.852439.6659
80.89590.29830.38034.1382.46822.9876-0.05320.0669-0.0047-0.4894-0.0394-0.0775-0.2117-0.03610.12470.3610.04090.01120.2333-0.04890.3345-4.6789-12.391135.9621
93.84861.324-0.48812.34490.6392.4305-0.34730.17630.1215-1.28410.5786-1.2158-0.64270.2358-0.24790.66-0.05440.06310.3652-0.08190.39171.262-5.466930.0355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 95 )
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 177 )
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 198 )
7X-RAY DIFFRACTION7chain 'A' and (resid 199 through 237 )
8X-RAY DIFFRACTION8chain 'A' and (resid 238 through 279 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 14 )

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