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- PDB-4css: Crystal structure of FimH in complex with a sulfonamide biphenyl ... -

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Basic information

Entry
Database: PDB / ID: 4css
TitleCrystal structure of FimH in complex with a sulfonamide biphenyl alpha D-mannoside
ComponentsPROTEIN FIMH
KeywordsSUGAR BINDING PROTEIN / FIMH ANTAGONISTS / TYPE I PILI / UTI / UPEC / ADHESIN
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-CWX / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.069 Å
AuthorsKleeb, S. / Pang, L. / Mayer, K. / Sigl, A. / Eris, D. / Preston, R.C. / Zihlmann, P. / Abgottspon, D. / Hutter, A. / Scharenberg, M. ...Kleeb, S. / Pang, L. / Mayer, K. / Sigl, A. / Eris, D. / Preston, R.C. / Zihlmann, P. / Abgottspon, D. / Hutter, A. / Scharenberg, M. / Jian, X. / Navarra, G. / Rabbani, S. / Smiesko, M. / Luedin, N. / Jakob, R.P. / Schwardt, O. / Maier, T. / Sharpe, T. / Ernst, B.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Fimh Antagonists: Bioisosteres to Improve the in Vitro and in Vivo Pk/Pd Profile.
Authors: Kleeb, S. / Pang, L. / Mayer, K. / Eris, D. / Sigl, A. / Preston, R.C. / Zihlmann, P. / Sharpe, T. / Jakob, R.P. / Abgottspon, D. / Hutter, A.S. / Scharenberg, M. / Jiang, X. / Navarra, G. / ...Authors: Kleeb, S. / Pang, L. / Mayer, K. / Eris, D. / Sigl, A. / Preston, R.C. / Zihlmann, P. / Sharpe, T. / Jakob, R.P. / Abgottspon, D. / Hutter, A.S. / Scharenberg, M. / Jiang, X. / Navarra, G. / Rabbani, S. / Smiesko, M. / Ludin, N. / Bezencon, J. / Schwardt, O. / Maier, T. / Ernst, B.
History
DepositionMar 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 2.0Aug 23, 2017Group: Atomic model / Data collection / Category: atom_site / diffrn_detector
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn_detector.type
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9583
Polymers17,4401
Non-polymers5182
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.384, 56.234, 61.595
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 PROTEIN FIMH / FIMH


Mass: 17440.479 Da / Num. of mol.: 1 / Fragment: LECTIN DOMAIN, RESIDUES 22-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HM125 / References: UniProt: P08191
#2: Chemical ChemComp-CWX / 4'-(alpha-D-Mannopyranosyloxy)-biphenyl-4-methyl sulfonamide


Mass: 425.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23NO8S
#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.: 326 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 4.7
Details: 0.2 M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 20% W/V PEG 3,350, pH 4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999
DetectorType: DECTRIS PILATUS 2M-F / 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: 1.07→30 Å / Num. obs: 72000 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Biso Wilson estimate: 9.95 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.5
Reflection shellResolution: 1.07→1.13 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / % possible all: 78

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UWF

1uwf


Resolution: 1.069→28.117 Å / SU ML: 0.08 / σ(F): 1.37 / Phase error: 10.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1321 3613 5 %
Rwork0.1123 --
obs0.1133 71998 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.069→28.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 35 326 1539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121504
X-RAY DIFFRACTIONf_angle_d1.6152093
X-RAY DIFFRACTIONf_dihedral_angle_d11.744534
X-RAY DIFFRACTIONf_chiral_restr0.378232
X-RAY DIFFRACTIONf_plane_restr0.009277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.069-1.0830.284800.28751562X-RAY DIFFRACTION57
1.083-1.09790.2545970.24672007X-RAY DIFFRACTION74
1.0979-1.11350.26211200.20112328X-RAY DIFFRACTION86
1.1135-1.13020.1911560.16322416X-RAY DIFFRACTION91
1.1302-1.14780.13841540.13432606X-RAY DIFFRACTION96
1.1478-1.16670.14811220.11832636X-RAY DIFFRACTION97
1.1667-1.18680.1221490.11362654X-RAY DIFFRACTION98
1.1868-1.20830.11971190.10392681X-RAY DIFFRACTION98
1.2083-1.23160.12431610.10622674X-RAY DIFFRACTION100
1.2316-1.25670.14051490.09722690X-RAY DIFFRACTION99
1.2567-1.28410.11761340.09522743X-RAY DIFFRACTION100
1.2841-1.31390.10431350.09162686X-RAY DIFFRACTION100
1.3139-1.34680.10751400.08962745X-RAY DIFFRACTION100
1.3468-1.38320.10121510.08762713X-RAY DIFFRACTION100
1.3832-1.42390.13281460.0852734X-RAY DIFFRACTION100
1.4239-1.46990.10141450.08012713X-RAY DIFFRACTION100
1.4699-1.52240.0911310.07982741X-RAY DIFFRACTION100
1.5224-1.58330.10541340.07632737X-RAY DIFFRACTION100
1.5833-1.65540.09361410.08562760X-RAY DIFFRACTION100
1.6554-1.74260.11340.09332745X-RAY DIFFRACTION100
1.7426-1.85180.11241380.10222768X-RAY DIFFRACTION100
1.8518-1.99480.13561720.10342721X-RAY DIFFRACTION100
1.9948-2.19540.12511690.10792766X-RAY DIFFRACTION100
2.1954-2.51290.12891440.11672781X-RAY DIFFRACTION100
2.5129-3.16530.15291390.12622816X-RAY DIFFRACTION100
3.1653-28.12670.15061530.12872962X-RAY DIFFRACTION100

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