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- PDB-5mts: Complex of FimH lectin with a TazMan (thiazolylaminomannosides) f... -

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Basic information

Entry
Database: PDB / ID: 5mts
TitleComplex of FimH lectin with a TazMan (thiazolylaminomannosides) family member known as potent anti-adhesive agent at 2.6 A resolution
ComponentsProtein FimH
KeywordsCELL ADHESION / BACTERIAL ADHESIN / TYPE 1 FIMBRIAE / URINARY TRACT INFECTION / CROHN'S DISEASE
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
NICKEL (II) ION / Chem-XKA / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
Authorsde Ruyck, J. / Bouckaert, J.
CitationJournal: ChemMedChem / Year: 2017
Title: Physiochemical Tuning of Potent Escherichia coli Anti-Adhesives by Microencapsulation and Methylene Homologation.
Authors: Alvarez Dorta, D. / Chalopin, T. / Sivignon, A. / de Ruyck, J. / Dumych, T.I. / Bilyy, R.O. / Deniaud, D. / Barnich, N. / Bouckaert, J. / Gouin, S.G.
History
DepositionJan 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Oct 16, 2019Group: Atomic model / Data collection / Category: atom_site / reflns_shell / Item: _atom_site.occupancy
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein FimH
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0256
Polymers62,9772
Non-polymers1,0484
Water5,585310
1
A: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0123
Polymers31,4881
Non-polymers5242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0123
Polymers31,4881
Non-polymers5242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.277, 90.277, 97.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-558-

HOH

21A-559-

HOH

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Components

#1: Protein Protein FimH


Mass: 31488.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli (E. coli) / References: UniProt: P08191
#2: Chemical ChemComp-XKA / [2-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]amino]-1,3-thiazol-5-yl]-(4-methyl-2-pyrazin-2-yl-1,3-thiazol-5-yl)methanone


Mass: 465.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19N5O6S2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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

Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.0 M LI2SO4 0.1 M TRIS-HCL 0.01 M NICL2 3% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 12883 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 7.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UWF

1uwf


Resolution: 2.6→45.139 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 1282 9.95 %
Rwork0.1699 --
obs0.1779 12883 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→45.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 64 310 2766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082534
X-RAY DIFFRACTIONf_angle_d1.0793495
X-RAY DIFFRACTIONf_dihedral_angle_d15.5711451
X-RAY DIFFRACTIONf_chiral_restr0.056407
X-RAY DIFFRACTIONf_plane_restr0.007449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70410.38761390.31411248X-RAY DIFFRACTION100
2.7041-2.82710.37311300.27481281X-RAY DIFFRACTION100
2.8271-2.97620.35391540.23711249X-RAY DIFFRACTION100
2.9762-3.16260.28111400.2241282X-RAY DIFFRACTION100
3.1626-3.40670.25211400.17541264X-RAY DIFFRACTION100
3.4067-3.74940.22571380.15011302X-RAY DIFFRACTION100
3.7494-4.29160.22571490.13321281X-RAY DIFFRACTION100
4.2916-5.40550.19711430.12011308X-RAY DIFFRACTION99
5.4055-45.14530.22011490.15811386X-RAY DIFFRACTION98

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