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- PDB-3zl2: A thiazolyl-mannoside bound to FimH, orthorhombic space group -

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Basic information

Entry
Database: PDB / ID: 3zl2
TitleA thiazolyl-mannoside bound to FimH, orthorhombic space group
ComponentsPROTEIN FIMH
KeywordsCELL ADHESION / TYPE-1 FIMBRIAE / THIAZOLE / CROHN'S DISEASE / IMMUNOGLOBULIN
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-BWG / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.251 Å
AuthorsBrument, S. / Sivignon, A. / Dumych, T.I. / Moreau, N. / Roos, G. / Guerardel, Y. / Chalopin, T. / Deniaud, D. / Bilyy, R.O. / Darfeuille-Michaud, A. ...Brument, S. / Sivignon, A. / Dumych, T.I. / Moreau, N. / Roos, G. / Guerardel, Y. / Chalopin, T. / Deniaud, D. / Bilyy, R.O. / Darfeuille-Michaud, A. / Bouckaert, J. / Gouin, S.G.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Thiazolylaminomannosides as Potent Antiadhesives of Type 1 Piliated Escherichia Coli Isolated from Crohn'S Disease Patients.
Authors: Brument, S. / Sivignon, A. / Dumych, T.I. / Moreau, N. / Roos, G. / Guerardel, Y. / Chalopin, T. / Deniaud, D. / Bilyy, R.O. / Darfeuille-Michaud, A. / Bouckaert, J. / Gouin, S.G.
History
DepositionJan 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_database_status / struct_site / struct_site_gen
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 / _chem_comp.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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: PROTEIN FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2212
Polymers16,9171
Non-polymers3041
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.460, 95.050, 28.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2123-

HOH

21A-2131-

HOH

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Components

#1: Protein PROTEIN FIMH


Mass: 16916.828 Da / Num. of mol.: 1
Fragment: LECTIN DOMAIN OR RECEPTOR BINDING DOMAIN, RESIDUES 22-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P08191
#2: Sugar ChemComp-BWG / N-{5-[(1R)-1-hydroxyethyl]-1,3-thiazol-2-yl}-alpha-D-mannopyranosylamine / N-{5-[(1R)-1-hydroxyethyl]-1,3-thiazol-2-yl}-alpha-D-mannosylamine / N-{5-[(1R)-1-hydroxyethyl]-1,3-thiazol-2-yl}-D-mannosylamine / N-{5-[(1R)-1-hydroxyethyl]-1,3-thiazol-2-yl}-mannosylamine


Type: D-saccharide / Mass: 304.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.77 Å3/Da / Density % sol: 55.6 % / Description: NONE
Crystal growpH: 6.5
Details: 20 MM NA/K PHOSPHATE, 0.1 M BIS TRIS PROPANE PH 6.5, 20 % (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.25→32.62 Å / Num. obs: 52365 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 11.42 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.08
Reflection shellResolution: 1.25→1.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.39 / % possible all: 93.8

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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: 1.251→32.621 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 16.97 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1878 2619 5 %
Rwork0.1684 --
obs0.1694 52362 98.53 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.004 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 13.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.1213 Å20 Å20 Å2
2---3.4312 Å20 Å2
3---2.3099 Å2
Refinement stepCycle: LAST / Resolution: 1.251→32.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 20 375 1591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091273
X-RAY DIFFRACTIONf_angle_d1.5621760
X-RAY DIFFRACTIONf_dihedral_angle_d12.494445
X-RAY DIFFRACTIONf_chiral_restr0.096209
X-RAY DIFFRACTIONf_plane_restr0.007227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2507-1.27340.25311180.26772239X-RAY DIFFRACTION86
1.2734-1.29790.25751330.2512515X-RAY DIFFRACTION96
1.2979-1.32440.26821350.23932582X-RAY DIFFRACTION99
1.3244-1.35320.2531390.23442624X-RAY DIFFRACTION100
1.3532-1.38470.23451360.22282589X-RAY DIFFRACTION100
1.3847-1.41930.23211400.20682656X-RAY DIFFRACTION99
1.4193-1.45770.24061350.19552574X-RAY DIFFRACTION100
1.4577-1.50060.21651410.18452666X-RAY DIFFRACTION100
1.5006-1.5490.17681360.17452596X-RAY DIFFRACTION100
1.549-1.60440.16921380.16742618X-RAY DIFFRACTION100
1.6044-1.66860.16561390.15552643X-RAY DIFFRACTION99
1.6686-1.74460.1681380.15712623X-RAY DIFFRACTION100
1.7446-1.83650.1771390.15852634X-RAY DIFFRACTION99
1.8365-1.95160.17161390.15452646X-RAY DIFFRACTION100
1.9516-2.10230.15671380.15292626X-RAY DIFFRACTION99
2.1023-2.31380.17371410.14742674X-RAY DIFFRACTION99
2.3138-2.64840.16821410.15112682X-RAY DIFFRACTION99
2.6484-3.33620.18341420.15322689X-RAY DIFFRACTION99
3.3362-32.63170.19371510.17132867X-RAY DIFFRACTION99

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