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- PDB-5l4t: Crystal structure of FimH lectin domain in complex with 2-Deoxy-H... -

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Basic information

Entry
Database: PDB / ID: 5l4t
TitleCrystal structure of FimH lectin domain in complex with 2-Deoxy-Heptylmannoside
ComponentsProtein FimH
KeywordsSUGAR BINDING PROTEIN / FimH / Type 1 pilus / urinary tract infection / UTI / carbohydrate / lectin / mannose / cell adhesion
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
heptyl 2-deoxy-alpha-D-mannopyranoside / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJakob, R.P. / Zihlmann, P. / Rabbani, S. / Maier, T. / Ernst, B.
CitationJournal: To Be Published
Title: High-Affinity Carbohydrate-Lectin Interactions: How Nature Makes it Possible
Authors: Zihlmann, P. / Jiang, X. / Sager, C.P. / Fiege, B. / Jakob, R.P. / Siegrist, S. / Zalewski, A. / Rabbani, S. / Eris, D. / Silbermann, M. / Pang, L. / Muhlethaler, T. / Sharpe, T. / Maier, T. / Ernst, B.
History
DepositionMay 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
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 / _atom_site.occupancy / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 5, 2020Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.2Jan 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 2.3Nov 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: Protein FimH
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3584
Polymers33,8342
Non-polymers5252
Water7,710428
1
A: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1792
Polymers16,9171
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1792
Polymers16,9171
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.760, 68.570, 96.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-593-

HOH

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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 K12 (bacteria) / Gene: fimH, b4320, JW4283 / Plasmid: pTRC99a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08191
#2: Sugar ChemComp-6LS / heptyl 2-deoxy-alpha-D-mannopyranoside / 2-Deoxy-Heptylmannoside / heptyl 2-deoxy-alpha-D-mannoside / heptyl 2-deoxy-D-mannoside / heptyl 2-deoxy-mannoside


Type: D-saccharide / Mass: 262.343 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C13H26O5 / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimH / Plasmid: pTRC99a / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M (NH4)2SO4, 0.1 M Hepes pH 7 and 25-30% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.9→55.38 Å / Num. obs: 35495 / % possible obs: 98.5 % / Redundancy: 5.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.175 / Net I/σ(I): 7
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 1.5 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIXdev_1938refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XO8

4xo8


Resolution: 1.9→55.38 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2178 1667 4.7 %
Rwork0.2005 --
obs0.2013 35495 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→55.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 36 428 2856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042506
X-RAY DIFFRACTIONf_angle_d0.9693448
X-RAY DIFFRACTIONf_dihedral_angle_d10.362884
X-RAY DIFFRACTIONf_chiral_restr0.044406
X-RAY DIFFRACTIONf_plane_restr0.004444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.9560.36461500.32772763X-RAY DIFFRACTION98
1.956-2.01920.30431420.28022760X-RAY DIFFRACTION99
2.0192-2.09130.26761340.26072803X-RAY DIFFRACTION99
2.0913-2.17510.20961290.22622791X-RAY DIFFRACTION99
2.1751-2.27410.28351310.21362814X-RAY DIFFRACTION99
2.2741-2.39390.21261160.20972830X-RAY DIFFRACTION99
2.3939-2.54390.25281390.20622819X-RAY DIFFRACTION99
2.5439-2.74030.24721750.19532805X-RAY DIFFRACTION99
2.7403-3.01610.19331270.19892850X-RAY DIFFRACTION99
3.0161-3.45250.21881500.18192842X-RAY DIFFRACTION99
3.4525-4.34950.18481360.16922861X-RAY DIFFRACTION98
4.3495-55.380.16241380.17652890X-RAY DIFFRACTION95
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)
10.42640.3348-0.65840.3257-0.11513.1584-0.02040.0458-0.0142-0.01290.05660.01950.4077-0.2502-0.05750.2451-0.0532-0.02130.18950.00950.249119.234669.321998.4649
21.77870.5556-2.35260.90820.1514.15470.1620.02920.22480.0449-0.09060.1686-0.3798-0.2509-0.12050.22020.02060.01220.19950.01550.220819.52580.0157104.7822
30.3302-0.6313-0.84432.16691.46643.20370.03640.113-0.0229-0.0753-0.08250.15030.0151-0.16380.02990.1495-0.01290.00030.16730.00350.174326.531676.653597.1047
40.7392-0.0692-0.05720.2913-0.13811.9881-0.0338-0.01410.00810.0090.03930.04370.1002-0.3107-0.07560.1883-0.0197-0.01380.17850.00150.204616.077175.9284104.1971
50.5463-0.18170.79880.5483-1.0643.1047-0.0157-0.04280.05050.0389-0.03440.0607-0.4909-0.15390.020.22340.0705-0.00620.21350.00790.2417.1622102.391124.5883
60.7117-0.02521.05120.65070.1561.71380.0842-0.07670.0132-0.0308-0.0169-0.01830.1377-0.1411-0.00240.16650.05010.02010.21810.01280.208521.881595.3889130.5328
70.37730.4460.76922.49022.40712.70450.06710.26260.0688-0.00890.1076-0.02470.09290.2275-0.13620.26150.0534-0.01570.2256-0.01930.237326.987790.3276127.562
81.69181.15122.77591.84613.02018.5218-0.01890.08480.13-0.01930.01510.139-0.09550.20810.1320.15010.04340.01240.1178-0.00650.211423.423198.7462123.9126
90.20950.00390.11340.2932-0.58982.42680.04270.0162-0.0073-0.04910.03780.04410.0755-0.0849-0.02280.15470.0346-0.01090.18530.00650.191515.376895.8433126.9242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 158 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 40 )
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 77 )
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 95 )
8X-RAY DIFFRACTION8chain 'B' and (resid 96 through 116 )
9X-RAY DIFFRACTION9chain 'B' and (resid 117 through 158 )

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