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- PDB-5muc: Crystal structure of the FimH lectin domain in complex with 1,5-A... -

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Basic information

Entry
Database: PDB / ID: 5muc
TitleCrystal structure of the FimH lectin domain in complex with 1,5-Anhydromannitol
ComponentsProtein FimH
KeywordsSUGAR BINDING PROTEIN / FimH / UTI / lectin / carbohydrate / UPEC / bladder infection
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
1-deoxy-alpha-D-mannopyranose / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJakob, R.P. / Rabbani, S. / Ernst, B. / Maier, T.
CitationJournal: Chemistry / Year: 2018
Title: KinITC-One Method Supports both Thermodynamic and Kinetic SARs as Exemplified on FimH Antagonists.
Authors: Zihlmann, P. / Silbermann, M. / Sharpe, T. / Jiang, X. / Muhlethaler, T. / Jakob, R.P. / Rabbani, S. / Sager, C.P. / Frei, P. / Pang, L. / Maier, T. / Ernst, B.
History
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.3Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein FimH
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1624
Polymers33,8342
Non-polymers3282
Water4,648258
1
A: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0812
Polymers16,9171
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0812
Polymers16,9171
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.382, 68.564, 95.687
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: 16916.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fimH, b4320, JW4283 / Plasmid: pTRC99a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08191
#2: Sugar ChemComp-AH2 / 1-deoxy-alpha-D-mannopyranose / 1,5-Anhydromannitol / 1-deoxy-alpha-D-mannose / 1-deoxy-D-mannose / 1-deoxy-mannose


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Ammoniumsulfat, 0.1 M Hepes 7.5, 1% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.87287 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.87287 Å / Relative weight: 1
ReflectionResolution: 2.6→47.843 Å / Num. obs: 12481 / % possible obs: 94.98 % / Redundancy: 4.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.0196 / Net I/σ(I): 6
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2 / Num. unique obs: 1322 / CC1/2: 0.707 / % possible all: 96.2

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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: 5CJQ

5cjq


Resolution: 2.6→47.843 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 675 5.41 %
Rwork0.2346 --
obs0.2361 12481 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→47.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 22 258 2672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032476
X-RAY DIFFRACTIONf_angle_d0.7053406
X-RAY DIFFRACTIONf_dihedral_angle_d11.8851442
X-RAY DIFFRACTIONf_chiral_restr0.051402
X-RAY DIFFRACTIONf_plane_restr0.003438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80070.31311210.29992330X-RAY DIFFRACTION95
2.8007-3.08250.28431570.27492337X-RAY DIFFRACTION97
3.0825-3.52850.30091340.23332370X-RAY DIFFRACTION97
3.5285-4.4450.24111310.19922252X-RAY DIFFRACTION90
4.445-47.85160.21281320.21972517X-RAY DIFFRACTION96
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)
10.0510.15240.57740.61091.7346.0890.1271-0.01440.2043-0.01360.1873-0.0528-0.52970.1279-0.20470.5301-0.05620.0630.3441-0.01320.2755-14.1194-0.38428.717
20.45470.24631.31720.49440.67587.3447-0.14190.02670.1255-0.16680.1031-0.053-0.466-0.2893-0.03030.58060.0385-0.05310.2560.03420.2397-22.5996-1.2340.2059
31.0194-0.21362.00320.0596-0.22897.6270.021-0.0531-0.07060.1133-0.1336-0.07620.34540.24010.01980.5862-0.1186-0.00350.2751-0.00740.1102-18.1374-11.448811.3218
41.6314-1.21951.29342.7228-2.40755.0510.19060.1093-0.11980.10490.02230.35360.3711-0.3628-0.13940.5562-0.04820.05640.3266-0.0290.2035-25.1272-12.86376.8828
50.481-0.10640.71180.2494-0.53514.2618-0.0215-0.20660.0853-0.0105-0.06750.0348-0.1374-0.120.02630.67860.052-0.03430.34950.01580.0596-21.8532-4.246110.7539
62.08210.7118-3.59510.2539-1.34757.60910.0516-0.2467-0.05860.34510.0107-0.16620.1740.8839-0.09050.5205-0.04220.00240.411-0.0270.1789-6.6254-3.47222.9669
71.30070.28521.53460.66620.76254.98780.05880.137-0.1585-0.03120.07850.02890.39890.2292-0.06450.59070.01230.04070.3168-0.02620.1428-15.9096-9.4844-0.5738
82.75630.11320.44530.74720.94673.22280.0344-0.2384-0.09950.239-0.08260.0117-0.00810.16810.08240.5958-0.00740.02250.21850.03820.1461-10.9001-0.584726.9444
92.81721.2681-1.27444.1354-3.3077.3612-0.0357-0.3219-0.46860.25110.11460.09090.7679-0.2897-0.05790.4925-0.0217-0.01470.32280.08970.2215-48.3701-0.12013.9219
100.41120.0369-0.70430.8855-0.69826.1163-0.0052-0.01780.09540.4353-0.12920.16710.2543-0.15140.05310.53190.00450.06080.3568-0.0240.2026-48.44780.788524.8595
110.31030.0696-1.22140.38060.26156.3728-0.18810.10030.01520.1316-0.0090.05090.41020.130.0410.6251-0.0001-0.01120.3009-0.01570.2183-39.8581.22216.8461
121.24260.0135-1.79970.13510.27844.73310.23320.26630.16530.1034-0.10450.0967-0.386-0.1841-0.07780.6029-0.04940.02980.257-0.0130.1332-44.271611.420617.9581
131.292-0.2712-0.55561.96691.83461.7810.11130.2032-0.0984-0.31190.2063-0.4631-0.4390.3452-0.27480.5762-0.02170.04150.3553-0.01770.2118-37.294112.828213.5387
140.6543-0.3684-2.20990.20891.25697.5394-0.17010.124-0.0820.0152-0.1192-0.05070.52650.39730.16970.52020.02860.02360.24870.01680.2462-37.2537-0.34.4646
151.1155-0.4058-0.94460.63380.731.6190.0775-0.13940.01310.05680.07180.0260.02360.20420.07090.6987-0.03490.08730.3946-0.06810.0294-43.84578.455229.5897
163.46610.91535.07210.24511.38278.02980.0122-0.30490.02730.349-0.19290.0696-0.1772-1.02150.17210.5815-0.04880.06730.245-0.03390.1747-55.74633.54429.6245
170.88360.1298-1.120.5224-0.48544.03380.12160.03250.16810.04660.0410.0255-0.2963-0.1230.02050.53130.0072-0.0190.32980.00810.126-47.59267.590711.9988
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 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 124 )
7X-RAY DIFFRACTION7chain 'A' and (resid 125 through 150 )
8X-RAY DIFFRACTION8chain 'A' and (resid 151 through 158 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 15 )
10X-RAY DIFFRACTION10chain 'B' and (resid 16 through 32 )
11X-RAY DIFFRACTION11chain 'B' and (resid 33 through 53 )
12X-RAY DIFFRACTION12chain 'B' and (resid 54 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 95 )
14X-RAY DIFFRACTION14chain 'B' and (resid 96 through 104 )
15X-RAY DIFFRACTION15chain 'B' and (resid 105 through 116 )
16X-RAY DIFFRACTION16chain 'B' and (resid 117 through 124 )
17X-RAY DIFFRACTION17chain 'B' and (resid 125 through 158 )

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