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- PDB-4av0: Structure of the FimH lectin domain in the trigonal space group, ... -

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Basic information

Entry
Database: PDB / ID: 4av0
TitleStructure of the FimH lectin domain in the trigonal space group, in complex with a methoxy phenyl propynyl alpha-D-mannoside at 2.1 A 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-HNV / 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: 2.099 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 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Atomic model / Derived calculations / Other
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_database_status.status_code_sf / _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 1.4Dec 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)34,6967
Polymers33,8342
Non-polymers8625
Water5,639313
1
A: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3964
Polymers16,9171
Non-polymers4793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3003
Polymers16,9171
Non-polymers3832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.140, 91.140, 80.170
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-2112-

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-HNV / 3-(4-methoxyphenyl)prop-2-yn-1-yl alpha-D-mannopyranoside / 3-(4-methoxyphenyl)prop-2-yn-1-yl alpha-D-mannoside / 3-(4-methoxyphenyl)prop-2-yn-1-yl D-mannoside / 3-(4-methoxyphenyl)prop-2-yn-1-yl mannoside


Type: D-saccharide / Mass: 324.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20O7
#3: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56 % / 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.873
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.012
ReflectionResolution: 2.1→19.79 Å / Num. obs: 22734 / % possible obs: 90.8 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 24.67 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.55
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2 / % possible all: 79.7

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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: 2.099→19.793 Å / SU ML: 0.31 / σ(F): 2.01 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1137 5 %
Rwork0.1738 --
obs0.1767 22733 99.78 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.789 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.2626 Å20 Å20 Å2
2--0.2626 Å20 Å2
3----0.5252 Å2
Refinement stepCycle: LAST / Resolution: 2.099→19.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 53 313 2758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152546
X-RAY DIFFRACTIONf_angle_d1.5413518
X-RAY DIFFRACTIONf_dihedral_angle_d20.706917
X-RAY DIFFRACTIONf_chiral_restr0.078412
X-RAY DIFFRACTIONf_plane_restr0.005447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0994-2.19480.3441370.27642604X-RAY DIFFRACTION98
2.1948-2.31040.3211400.25662660X-RAY DIFFRACTION100
2.3104-2.45490.32411420.22222697X-RAY DIFFRACTION100
2.4549-2.6440.29361410.20942691X-RAY DIFFRACTION100
2.644-2.90930.2321410.18142674X-RAY DIFFRACTION100
2.9093-3.32860.23311420.15252698X-RAY DIFFRACTION100
3.3286-4.18710.15991450.13672746X-RAY DIFFRACTION100
4.1871-19.79340.18681490.13972826X-RAY DIFFRACTION100

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