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

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Basic information

Entry
Database: PDB / ID: 4avi
TitleStructure of the FimH lectin domain in the trigonal space group, in complex with a methyl ester octyl alpha-D-mannoside at 2.4 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
NICKEL (II) ION / METHYL ESTER OCTYL ALPHA-1O-D-MANNOPYRANNOSIDE / 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 1.1Jul 18, 2012Group: Atomic model / Derived calculations / Other
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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)34,7487
Polymers33,8342
Non-polymers9145
Water5,675315
1
A: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4224
Polymers16,9171
Non-polymers5053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3263
Polymers16,9171
Non-polymers4092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.620, 90.620, 79.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: Chemical ChemComp-XNS / METHYL ESTER OCTYL ALPHA-1O-D-MANNOPYRANNOSIDE


Mass: 350.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30O8
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.78 Å3/Da / Density % sol: 55.76 % / 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: Feb 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.4→18.64 Å / Num. obs: 15111 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 24.75 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.01
Reflection shellResolution: 2.4→2.6 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4 / % possible all: 89.3

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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→18.64 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 756 5 %
Rwork0.1398 --
obs0.1435 15107 99.91 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.604 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.1764 Å20 Å20 Å2
2---0.1764 Å20 Å2
3---0.3529 Å2
Refinement stepCycle: LAST / Resolution: 2.4→18.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 55 315 2762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132535
X-RAY DIFFRACTIONf_angle_d1.4883489
X-RAY DIFFRACTIONf_dihedral_angle_d12.307893
X-RAY DIFFRACTIONf_chiral_restr0.109409
X-RAY DIFFRACTIONf_plane_restr0.005445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.5850.28051490.17752830X-RAY DIFFRACTION100
2.585-2.84430.24431490.16242822X-RAY DIFFRACTION100
2.8443-3.2540.25131500.1382853X-RAY DIFFRACTION100
3.254-4.09250.18271510.12832875X-RAY DIFFRACTION100
4.0925-18.64050.17961570.12842971X-RAY DIFFRACTION100

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