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- PDB-5fx3: Breaking down the wall: mutation of the tyrosine gate of the univ... -

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Basic information

Entry
Database: PDB / ID: 5fx3
TitleBreaking down the wall: mutation of the tyrosine gate of the universal Escherichia coli fimbrial adhesin FimH
ComponentsFimH
KeywordsCELL ADHESION / BACTERIAL ADHESIN / TYPE 1 FIMBRIAE / URINARY TRACT INFECTION / VARIABLE IMMUNOGLOBULIN FOLD
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 / metal ion binding
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-EDT / Type 1 fimbrin D-mannose specific adhesin / FimH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBouckaert, J.
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
DepositionFeb 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_database_status / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_struct_mod_residue.details / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1582
Polymers16,8661
Non-polymers2921
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.180, 54.180, 257.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2070-

HOH

21A-2144-

HOH

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Components

#1: Protein FimH


Mass: 16865.762 Da / Num. of mol.: 1 / Fragment: FIMH LECTIN DOMAIN, RESIDUES 22-179 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimH / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9S497, UniProt: P08191*PLUS
#2: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
Sequence detailsY137A MUTATION

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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: 3.21 Å3/Da / Density % sol: 61.76 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M SODIUM MALONATE 0.1 M BIS TRIS PROPANE PH 7.5 20 % W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.82→46.92 Å / Num. obs: 21963 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 17.64 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.27
Reflection shellResolution: 1.91→2.04 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 2.8 / % possible all: 99.7

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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: 1.9→46.921 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 939 5 %
Rwork0.1584 --
obs0.1606 18767 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.68 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 20 308 1520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011323
X-RAY DIFFRACTIONf_angle_d1.1141826
X-RAY DIFFRACTIONf_dihedral_angle_d12.447790
X-RAY DIFFRACTIONf_chiral_restr0.064208
X-RAY DIFFRACTIONf_plane_restr0.008241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-2.00030.3291300.28022468X-RAY DIFFRACTION100
2.0003-2.12560.24141290.21542449X-RAY DIFFRACTION99
2.1256-2.28980.20751310.16732489X-RAY DIFFRACTION100
2.2898-2.52020.21661320.15872510X-RAY DIFFRACTION100
2.5202-2.88480.22261330.15192532X-RAY DIFFRACTION100
2.8848-3.63430.18081370.1282599X-RAY DIFFRACTION100
3.6343-46.93550.1551470.13232781X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.6199 Å / Origin y: -15.2282 Å / Origin z: 3.7566 Å
111213212223313233
T0.1673 Å2-0.0084 Å2-0.027 Å2-0.0416 Å2-0.0067 Å2--0.1211 Å2
L1.7827 °20.4797 °2-1.4227 °2-1.2489 °2-0.5587 °2--3.5744 °2
S0.187 Å °0.0121 Å °0.0122 Å °-0.039 Å °-0.1368 Å °0.0157 Å °0.0997 Å °-0.0402 Å °-0.0117 Å °
Refinement TLS groupSelection details: ALL

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