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- PDB-5l4w: Crystal structure of FimH lectin domain in complex with 3-Fluoro-... -

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Basic information

Entry
Database: PDB / ID: 5l4w
TitleCrystal structure of FimH lectin domain in complex with 3-Fluoro-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 3-fluoro-alpha-D-mannopyranoside / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
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 1.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 10, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,5916
Polymers50,7503
Non-polymers8413
Water10,863603
1
A: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1972
Polymers16,9171
Non-polymers2801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1972
Polymers16,9171
Non-polymers2801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1972
Polymers16,9171
Non-polymers2801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.830, 95.340, 70.800
Angle α, β, γ (deg.)90.00, 105.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein FimH


Mass: 16916.828 Da / Num. of mol.: 3
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-6KH / heptyl 3-fluoro-alpha-D-mannopyranoside / 3-Fluoro-Heptylmannoside / heptyl 3-fluoro-alpha-D-mannoside / heptyl 3-fluoro-D-mannoside / heptyl 3-fluoro-mannoside


Type: D-saccharide / Mass: 280.333 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H25FO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.87 Å3/Da / Density % sol: 57.16 %
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→68.18 Å / Num. obs: 40710 / % possible obs: 90.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.67 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.2 / % possible all: 71.2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XO8

4xo8


Resolution: 1.9→68.18 Å / Cor.coef. Fo:Fc: 0.9427 / Cor.coef. Fo:Fc free: 0.9265 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 2063 5.07 %RANDOM
Rwork0.1723 ---
obs0.1739 40710 90.11 %-
Displacement parametersBiso mean: 27.14 Å2
Baniso -1Baniso -2Baniso -3
1--5.5658 Å20 Å2-5.2 Å2
2--4.6392 Å20 Å2
3---0.9266 Å2
Refine analyzeLuzzati coordinate error obs: 0.228 Å
Refinement stepCycle: LAST / Resolution: 1.9→68.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 57 603 4266
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013834HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.135349HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1392SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes552HARMONIC5
X-RAY DIFFRACTIONt_it3834HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.45
X-RAY DIFFRACTIONt_other_torsion14.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion522SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4639SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2647 100 4.68 %
Rwork0.2689 2037 -
all0.2687 2137 -
obs--90.11 %
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)
10.32890.34890.07631.9489-0.35470.48840.0165-0.007-0.0001-0.0141-0.0823-0.0421-0.05020.00920.06580.00150.0010.0062-0.0268-0.0019-0.033126.8552-7.165874.7599
20.2727-0.137-0.10752.2371-0.27330.12160.0606-0.0033-0.0010.0298-0.1006-0.0185-0.05650.02720.04-0.02450.0022-0.0103-0.0084-0.0055-0.022620.5819-33.59497.4504
30.99571.1852-0.6632.0699-0.89880.7713-0.0614-0.0221-0.0364-0.1042-0.0208-0.18460.11380.10330.0822-0.05850.00670.0013-0.03770.003-0.032523.8735-13.0982120.6336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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