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- PDB-4av5: Structure of a triclinic crystal of the FimH lectin domain in com... -

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Basic information

Entry
Database: PDB / ID: 4av5
TitleStructure of a triclinic crystal of the FimH lectin domain in complex with a propynyl biphenyl alpha-D-mannoside, at 1.4 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
Chem-FYZ / FimH / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 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 1.3Dec 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 / 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 / _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
C: FIMH
D: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,43711
Polymers67,6674
Non-polymers1,7707
Water20,7351151
1
A: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5755
Polymers16,9171
Non-polymers6594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2872
Polymers16,9171
Non-polymers3701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2872
Polymers16,9171
Non-polymers3701
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2872
Polymers16,9171
Non-polymers3701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.750, 51.520, 67.830
Angle α, β, γ (deg.)100.32, 93.17, 116.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
FIMH


Mass: 16916.828 Da / Num. of mol.: 4 / 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-FYZ / (2R,3S,4S,5S,6S)-2-(hydroxymethyl)-6-[3-(4-phenylphenyl)prop-2-ynoxy]oxane-3,4,5-triol


Mass: 370.396 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H22O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1151 / 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: 2.27 Å3/Da / Density % sol: 45.8 % / Description: NONE
Crystal growpH: 7.4 / Details: 2% PEG8000, 0.5 M LI2SO4, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.918
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.4→18.79 Å / Num. obs: 109811 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.86
Reflection shellResolution: 1.4→1.6 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.83 / % possible all: 86.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UWF

1uwf


Resolution: 1.4→18.592 Å / SU ML: 0.11 / σ(F): 2 / Phase error: 15.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1623 5490 5 %
Rwork0.1388 --
obs0.14 109799 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.123 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0.02 Å20.05 Å2
2---0.01 Å20.01 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→18.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 123 1151 6058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015208
X-RAY DIFFRACTIONf_angle_d1.4837201
X-RAY DIFFRACTIONf_dihedral_angle_d13.9831817
X-RAY DIFFRACTIONf_chiral_restr0.158842
X-RAY DIFFRACTIONf_plane_restr0.008926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.22151830.18583472X-RAY DIFFRACTION92
1.4159-1.43260.18671790.17083405X-RAY DIFFRACTION92
1.4326-1.450.171830.16873475X-RAY DIFFRACTION92
1.45-1.46840.20731800.16713434X-RAY DIFFRACTION92
1.4684-1.48770.20531810.16433427X-RAY DIFFRACTION93
1.4877-1.50810.18891810.15813447X-RAY DIFFRACTION93
1.5081-1.52960.18721800.16163406X-RAY DIFFRACTION92
1.5296-1.55240.20641800.1563422X-RAY DIFFRACTION92
1.5524-1.57670.17321850.1513523X-RAY DIFFRACTION94
1.5767-1.60250.17931830.14583470X-RAY DIFFRACTION93
1.6025-1.63010.18111840.14473494X-RAY DIFFRACTION94
1.6301-1.65970.16421820.14653475X-RAY DIFFRACTION94
1.6597-1.69160.18331850.14783504X-RAY DIFFRACTION94
1.6916-1.72610.17411810.1473447X-RAY DIFFRACTION93
1.7261-1.76360.18881850.14623507X-RAY DIFFRACTION94
1.7636-1.80460.16231850.14083525X-RAY DIFFRACTION94
1.8046-1.84970.1881870.13863535X-RAY DIFFRACTION95
1.8497-1.89970.16071820.13353465X-RAY DIFFRACTION94
1.8997-1.95550.14691810.13463438X-RAY DIFFRACTION93
1.9555-2.01860.1441870.12583557X-RAY DIFFRACTION95
2.0186-2.09060.15461820.12823457X-RAY DIFFRACTION93
2.0906-2.17420.14581860.1253527X-RAY DIFFRACTION94
2.1742-2.2730.15951830.12523488X-RAY DIFFRACTION94
2.273-2.39260.14381860.1273525X-RAY DIFFRACTION95
2.3926-2.54220.14381850.13143529X-RAY DIFFRACTION94
2.5422-2.73790.16341860.13533519X-RAY DIFFRACTION94
2.7379-3.01240.16161830.12553475X-RAY DIFFRACTION94
3.0124-3.44590.1331820.12043465X-RAY DIFFRACTION93
3.4459-4.33230.13591860.12973528X-RAY DIFFRACTION94
4.3323-18.59370.1881770.16863368X-RAY DIFFRACTION90

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