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- PDB-4avk: Structure of trigonal FimH lectin domain crystal soaked with an a... -

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Basic information

Entry
Database: PDB / ID: 4avk
TitleStructure of trigonal FimH lectin domain crystal soaked with an alpha- D-mannoside O-linked to propynyl pyridine at 2.4A resolution
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
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-FVQ / NICKEL (II) ION / FimH / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWellens, A. / Lahmann, M. / Touaibia, M. / Vaucher, J. / Oscarson, S. / Roy, R. / Remaut, H. / Bouckaert, J.
CitationJournal: Biochemistry / Year: 2012
Title: The Tyrosine Gate as a Potential Entropic Lever in the Receptor-Binding Site of the Bacterial Adhesin Fimh.
Authors: Wellens, A. / Lahmann, M. / Touaibia, M. / Vaucher, J. / Oscarson, S. / Roy, R. / Remaut, H. / Bouckaert, J.
History
DepositionMay 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _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.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_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 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:
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Assembly

Deposited unit
A: FIMH
B: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,92610
Polymers33,8342
Non-polymers1,0928
Water3,081171
1
A: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2713
Polymers16,9171
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6557
Polymers16,9171
Non-polymers7386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.460, 90.460, 79.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-2072-

HOH

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Components

#1: Protein FIMH


Mass: 16916.828 Da / Num. of mol.: 2 / Fragment: LECTIN DOMAIN, RESIDUES 10-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: UTI89 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A2IC68, UniProt: P08191*PLUS
#2: Sugar ChemComp-FVQ / 3-(pyridin-3-yl)prop-2-yn-1-yl alpha-D-mannopyranoside / 3-pyridin-3-ylprop-2-yn-1-yl alpha-D-mannopyranoside / D-MANNOSE ALPHA1O-PROPYNYL PYRIDINE / 3-(pyridin-3-yl)prop-2-yn-1-yl alpha-D-mannoside / 3-(pyridin-3-yl)prop-2-yn-1-yl D-mannoside / 3-(pyridin-3-yl)prop-2-yn-1-yl mannoside


Type: D-saccharide / Mass: 295.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H17NO6
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.76 Å3/Da / Density % sol: 55.51 % / Description: NONE
Crystal growpH: 8.6
Details: 1 M LI2SO4, 100 MM TRIS PH 8.6, 10 MM NICL2, 0.2 M NON-DETERGENT SULFOBETAINE 201

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.016
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.016 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 16232 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14
Reflection shellResolution: 2.4→2.6 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.2 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VCO

2vco


Resolution: 2.4→24.811 Å / SU ML: 0.26 / σ(F): 2.03 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2057 752 5 %
Rwork0.1661 --
obs0.1682 15043 99.9 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.133 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.1389 Å20 Å20 Å2
2---0.1389 Å20 Å2
3---0.2777 Å2
Refinement stepCycle: LAST / Resolution: 2.4→24.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 64 171 2627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112553
X-RAY DIFFRACTIONf_angle_d1.4483515
X-RAY DIFFRACTIONf_dihedral_angle_d19.777904
X-RAY DIFFRACTIONf_chiral_restr0.08411
X-RAY DIFFRACTIONf_plane_restr0.009449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.58520.26131470.20062808X-RAY DIFFRACTION100
2.5852-2.84510.23251490.1892822X-RAY DIFFRACTION100
2.8451-3.2560.22341490.16732843X-RAY DIFFRACTION100
3.256-4.09920.17271500.15542851X-RAY DIFFRACTION100
4.0992-24.8120.19381570.1552967X-RAY DIFFRACTION100

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