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- PDB-4ca4: Crystal structure of FimH lectin domain with the Tyr48Ala mutatio... -

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Basic information

Entry
Database: PDB / ID: 4ca4
TitleCrystal structure of FimH lectin domain with the Tyr48Ala mutation, in complex with heptyl alpha-D-mannopyrannoside
ComponentsFIMH
KeywordsCELL ADHESION / BACTERIAL ADHESIN / TYPE 1 FIMBRIAE / URINARY TRACT INFECTION / VARIABLE IMMUNOGLOBULIN FOLD / HEPTYL MANNOSE / FIMH ANTAGONIST
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 superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsRabbani, S. / Bouckaert, J. / Zalewski, A. / Preston, R. / Eid, S. / Thompson, A. / Puorger, C. / Glockshuber, R. / Ernst, B.
CitationJournal: IUCrJ / Year: 2017
Title: Mutation of Tyr137 of the universal Escherichia coli fimbrial adhesin FimH relaxes the tyrosine gate prior to mannose binding.
Authors: Rabbani, S. / Krammer, E.M. / Roos, G. / Zalewski, A. / Preston, R. / Eid, S. / Zihlmann, P. / Prevost, M. / Lensink, M.F. / Thompson, A. / Ernst, B. / Bouckaert, J.
History
DepositionOct 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references / Derived calculations
Revision 1.2Mar 15, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Jul 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 1.5Dec 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
B: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2064
Polymers33,6492
Non-polymers5572
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-7.4 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.850, 89.850, 91.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein FIMH


Mass: 16824.730 Da / Num. of mol.: 2 / Fragment: LECTIN DOMAIN, RESIDUES 10-167 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: UTI89 / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A2IC68
#2: 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.: 2 / Source method: obtained synthetically / Formula: C13H26O6 / Comment: detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.5
Details: 5% W/V PGA-LM 100 MM NA CACODYLATE PH 6.5 200 MM MGCL2 10 MM HM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.96
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 3.01→41 Å / Num. obs: 65358 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 43.15 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 8.58
Reflection shellResolution: 3.01→3.2 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 3.02 / % possible all: 99.1

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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 4AUU

4auu


Resolution: 2.84→40.9 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 23.39 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2442 459 5 %
Rwork0.1851 --
obs0.1882 9160 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 1 Å2 / ksol: 1 e/Å3
Displacement parametersBiso mean: 1 Å2
Refinement stepCycle: LAST / Resolution: 2.84→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 38 70 2486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012556
X-RAY DIFFRACTIONf_angle_d1.4513514
X-RAY DIFFRACTIONf_dihedral_angle_d13.483914
X-RAY DIFFRACTIONf_chiral_restr0.059421
X-RAY DIFFRACTIONf_plane_restr0.008448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-3.25080.32651490.24022819X-RAY DIFFRACTION98
3.2508-4.09510.2651520.17912882X-RAY DIFFRACTION99
4.0951-40.90420.2011580.16693000X-RAY DIFFRACTION98

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