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- PDB-4x5q: Crystal structure of FimH in complex with 5-nitro-indolinylphenyl... -

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Basic information

Entry
Database: PDB / ID: 4x5q
TitleCrystal structure of FimH in complex with 5-nitro-indolinylphenyl alpha-D-mannopyranoside
ComponentsProtein FimH
KeywordsSUGAR BINDING PROTEIN / Bacterial Adhesin / Pilus / UPEC / Antagonist Complex
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-3XN / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsPreston, R.C. / Jakob, R.P. / Fiege, B. / Zihlmann, P. / Rabbani, S. / Schwardt, O. / Jiang, X. / Ernst, B. / Maier, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_144183/1 Switzerland
CitationJournal: Chembiochem / Year: 2015
Title: The Tyrosine Gate of the Bacterial Lectin FimH: A Conformational Analysis by NMR Spectroscopy and X-ray Crystallography.
Authors: Fiege, B. / Rabbani, S. / Preston, R.C. / Jakob, R.P. / Zihlmann, P. / Schwardt, O. / Jiang, X. / Maier, T. / Ernst, B.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5032
Polymers17,0871
Non-polymers4161
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.460, 56.160, 61.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein FimH


Mass: 17087.039 Da / Num. of mol.: 1 / Fragment: UNP residues 22-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimH, b4320, JW4283 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / References: UniProt: P08191
#2: Chemical ChemComp-3XN / 4-(5-nitro-1H-indol-1-yl)phenyl alpha-D-mannopyranoside


Mass: 416.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 20% PEG 3,350, 0.2 M sodium phosphate monobasic monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→28.08 Å / Num. obs: 60363 / % possible obs: 92.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 39.9
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 7.1 / % possible all: 72.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1779)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UWF

1uwf


Resolution: 1.12→28.08 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1288 3042 5.04 %
Rwork0.106 --
obs0.1071 60362 92.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.12→28.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 30 300 1526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121364
X-RAY DIFFRACTIONf_angle_d1.5611886
X-RAY DIFFRACTIONf_dihedral_angle_d10.162500
X-RAY DIFFRACTIONf_chiral_restr0.326214
X-RAY DIFFRACTIONf_plane_restr0.009270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1196-1.13710.1803910.14651631X-RAY DIFFRACTION59
1.1371-1.15570.1476980.10481946X-RAY DIFFRACTION69
1.1557-1.17560.14151240.10142258X-RAY DIFFRACTION82
1.1756-1.1970.11261190.09312448X-RAY DIFFRACTION87
1.197-1.220.11921460.10592449X-RAY DIFFRACTION89
1.22-1.24490.14111250.11972554X-RAY DIFFRACTION91
1.2449-1.2720.13221400.09392557X-RAY DIFFRACTION92
1.272-1.30160.14861370.10832593X-RAY DIFFRACTION92
1.3016-1.33410.10691250.08772630X-RAY DIFFRACTION95
1.3341-1.37020.11581350.08052722X-RAY DIFFRACTION97
1.3702-1.41050.10911620.07662693X-RAY DIFFRACTION97
1.4105-1.45610.09951610.07562723X-RAY DIFFRACTION97
1.4561-1.50810.11081380.07612744X-RAY DIFFRACTION97
1.5081-1.56850.10561570.07282725X-RAY DIFFRACTION98
1.5685-1.63980.0971420.07552765X-RAY DIFFRACTION98
1.6398-1.72630.10921290.08292797X-RAY DIFFRACTION98
1.7263-1.83440.11241310.09322786X-RAY DIFFRACTION99
1.8344-1.9760.11831490.09712790X-RAY DIFFRACTION98
1.976-2.17480.11361270.09892857X-RAY DIFFRACTION99
2.1748-2.48930.11921540.11192811X-RAY DIFFRACTION99
2.4893-3.13570.13991890.12112847X-RAY DIFFRACTION99
3.1357-28.08880.15641630.13342994X-RAY DIFFRACTION99

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