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- PDB-6aow: Crystal structure of lectin domain of F9 pilus adhesin FmlH from ... -

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Basic information

Entry
Database: PDB / ID: 6aow
TitleCrystal structure of lectin domain of F9 pilus adhesin FmlH from E. coli UTI89
ComponentsF9 pilus adhesin FmlH
KeywordsSUGAR BINDING PROTEIN / Fimbrial adhesin / lectin / bacterial adhesion
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative Fml fimbrial adhesin FmlD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKalas, V. / Hultgren, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)108840 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2018
Title: Structure-based discovery of glycomimetic FmlH ligands as inhibitors of bacterial adhesion during urinary tract infection.
Authors: Kalas, V. / Hibbing, M.E. / Maddirala, A.R. / Chugani, R. / Pinkner, J.S. / Mydock-McGrane, L.K. / Conover, M.S. / Janetka, J.W. / Hultgren, S.J.
History
DepositionAug 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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 1.5Nov 20, 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: F9 pilus adhesin FmlH
B: F9 pilus adhesin FmlH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1285
Polymers35,8402
Non-polymers2883
Water4,720262
1
A: F9 pilus adhesin FmlH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0162
Polymers17,9201
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: F9 pilus adhesin FmlH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1123
Polymers17,9201
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.505, 78.340, 58.496
Angle α, β, γ (deg.)90.00, 96.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21B-374-

HOH

31B-386-

HOH

41B-427-

HOH

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Components

#1: Protein F9 pilus adhesin FmlH


Mass: 17920.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / UPEC / Gene: fmlD, UTI89_C1716 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q1RBS0
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1M NaCl, 0.1 M MES pH 5.6, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50.03 Å / Num. obs: 38073 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.057 / Rrim(I) all: 0.109 / Net I/σ(I): 8.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1891 / CC1/2: 0.382 / Rpim(I) all: 0.876 / Rrim(I) all: 1.648 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MCY

3mcy


Resolution: 1.6→50 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.85
RfactorNum. reflection% reflection
Rfree0.2334 1929 5.09 %
Rwork0.195 --
obs0.1969 37926 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 15 262 2579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062369
X-RAY DIFFRACTIONf_angle_d1.0873245
X-RAY DIFFRACTIONf_dihedral_angle_d10.812811
X-RAY DIFFRACTIONf_chiral_restr0.046371
X-RAY DIFFRACTIONf_plane_restr0.005411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.37331400.36532520X-RAY DIFFRACTION97
1.64-1.68440.3351230.33172556X-RAY DIFFRACTION98
1.6844-1.73390.34771230.29692615X-RAY DIFFRACTION99
1.7339-1.78990.30351640.2612560X-RAY DIFFRACTION99
1.7899-1.85390.29731540.24552568X-RAY DIFFRACTION99
1.8539-1.92810.27111280.22492595X-RAY DIFFRACTION99
1.9281-2.01590.20891500.18482612X-RAY DIFFRACTION100
2.0159-2.12220.21011340.17452630X-RAY DIFFRACTION100
2.1222-2.25510.23651360.1722589X-RAY DIFFRACTION100
2.2551-2.42920.22951400.17832627X-RAY DIFFRACTION99
2.4292-2.67370.22461310.18372600X-RAY DIFFRACTION99
2.6737-3.06050.23451380.18752551X-RAY DIFFRACTION98
3.0605-3.85570.17541300.16172455X-RAY DIFFRACTION93
3.8557-50.05570.22331380.17972519X-RAY DIFFRACTION94

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