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- PDB-5mca: Crystal structure of FimH-LD R60P variant in the apo state -

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Basic information

Entry
Database: PDB / ID: 5mca
TitleCrystal structure of FimH-LD R60P variant in the apo state
ComponentsProtein FimH
KeywordsSUGAR BINDING PROTEIN / FimH / type 1 pilus / pilus / UTI / urinary tract infection / bladder / Escherichia coli
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
Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.604 Å
AuthorsJakob, R.P. / Rabbani, S. / Ernst, B. / Maier, T.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Conformational switch of the bacterial adhesin FimH in the absence of the regulatory domain: Engineering a minimalistic allosteric system.
Authors: Rabbani, S. / Fiege, B. / Eris, D. / Silbermann, M. / Jakob, R.P. / Navarra, G. / Maier, T. / Ernst, B.
History
DepositionNov 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0102
Polymers16,9141
Non-polymers961
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-4 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.640, 57.193, 64.566
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: 16913.799 Da / Num. of mol.: 1 / Mutation: R60P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimH, b4320, JW4283 / Plasmid: pTRC99a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08191
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M (NH4)2SO4, 0.1M BisTris 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.604→42.812 Å / Num. obs: 46222 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Net I/σ(I): 27.3
Reflection shellResolution: 1.604→1.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7346 / CC1/2: 0.904 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2131: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X50

4x50


Resolution: 1.604→42.812 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.64
RfactorNum. reflection% reflection
Rfree0.1751 2336 5.05 %
Rwork0.1469 --
obs0.1484 46222 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.604→42.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 5 249 1450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081240
X-RAY DIFFRACTIONf_angle_d0.9011711
X-RAY DIFFRACTIONf_dihedral_angle_d11.158723
X-RAY DIFFRACTIONf_chiral_restr0.059199
X-RAY DIFFRACTIONf_plane_restr0.007222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6042-1.6370.3039990.24162472X-RAY DIFFRACTION95
1.637-1.67260.2751180.22672585X-RAY DIFFRACTION100
1.6726-1.71150.26031550.21372628X-RAY DIFFRACTION100
1.7115-1.75430.22191400.20132597X-RAY DIFFRACTION100
1.7543-1.80170.24271720.17662563X-RAY DIFFRACTION100
1.8017-1.85470.23341120.16462582X-RAY DIFFRACTION99
1.8547-1.91460.19571650.16822581X-RAY DIFFRACTION100
1.9146-1.9830.21771440.15522565X-RAY DIFFRACTION100
1.983-2.06240.17661610.14922566X-RAY DIFFRACTION100
2.0624-2.15630.16681510.13872614X-RAY DIFFRACTION100
2.1563-2.270.20861230.14132596X-RAY DIFFRACTION100
2.27-2.41220.17691090.13122583X-RAY DIFFRACTION100
2.4122-2.59840.16461290.14562604X-RAY DIFFRACTION100
2.5984-2.85980.1941410.14392595X-RAY DIFFRACTION100
2.8598-3.27350.1511480.14142574X-RAY DIFFRACTION100
3.2735-4.12380.15571440.12312600X-RAY DIFFRACTION100
4.1238-42.8120.13721250.14142581X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.19860.8875-0.7113.1476-0.02912.3073-0.01330.07290.0923-0.0008-0.0329-0.0402-0.06550.0001-0.01020.14750.02-0.00660.13240.00020.1672.952512.339673.3879
21.74270.8426-0.01352.46080.21971.72420.0777-0.08690.12080.1967-0.06240.323-0.0234-0.2163-0.03330.13280.02150.03160.1314-00.1714-2.98916.338478.8941
35.0631-1.7872-1.05024.72210.37352.5506-0.0812-0.07280.00250.00360.0503-0.1085-0.17050.11960.02850.1869-0.00320.02670.137-0.00650.13948.203125.419674.747
43.59683.36740.73744.30280.74861.96740.0085-0.3332-0.0220.0007-0.05920.3317-0.1046-0.37170.09430.18460.02480.02840.2260.04980.2708-5.462819.685180.1555
52.88280.535-1.78542.5168-0.60393.27370.244-0.09770.202-0.2269-0.1354-0.2196-0.4690.4264-0.05660.2142-0.03240.06760.16690.010.170411.956926.642367.093
62.15582.325-1.98594.7928-2.68083.8032-0.28480.1393-0.2257-0.1316-0.1033-0.37370.24320.19210.09880.1950.02530.07770.18620.02530.251416.777112.907966.5677
74.4818-0.2147-2.3583.15560.15913.91930.2073-0.15160.08750.4221-0.10070.1859-0.1349-0.12250.01610.2105-0.00710.01060.1052-0.00310.13093.220817.035583.7254
83.9838-0.1999-0.22351.9019-0.05583.20910.0037-0.6777-0.120.6578-0.03390.30480.0298-0.24330.14280.3033-0.0360.08840.21230.01660.1786-0.28214.29687.2105
91.81222.3104-0.24573.5673-1.10181.5764-0.1020.4511-0.2174-0.36820.07970.15980.4550.0093-0.06120.25190.01320.05780.2279-0.00630.208813.128316.548963.4034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 104 )
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 124 )
7X-RAY DIFFRACTION7chain 'A' and (resid 125 through 135 )
8X-RAY DIFFRACTION8chain 'A' and (resid 136 through 150 )
9X-RAY DIFFRACTION9chain 'A' and (resid 151 through 159 )

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