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- PDB-6arn: F9 pilus adhesin FmlH lectin domain from E. coli UTI89 co-crystal... -

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Basic information

Entry
Database: PDB / ID: 6arn
TitleF9 pilus adhesin FmlH lectin domain from E. coli UTI89 co-crystallized with o-methoxyphenyl beta-galactoside (OMPG)
ComponentsPutative Fml fimbrial adhesin FmlD
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
2-methoxyphenyl beta-D-galactopyranoside / Putative Fml fimbrial adhesin FmlD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
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 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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.mon_nstd_flag / _chem_comp.pdbx_synonyms / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: 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: Putative Fml fimbrial adhesin FmlD
B: Putative Fml fimbrial adhesin FmlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5095
Polymers35,8402
Non-polymers6693
Water6,305350
1
A: Putative Fml fimbrial adhesin FmlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3023
Polymers17,9201
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative Fml fimbrial adhesin FmlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2062
Polymers17,9201
Non-polymers2861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.263, 116.120, 50.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

21B-432-

HOH

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Components

#1: Protein Putative Fml fimbrial adhesin FmlD


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: Sugar ChemComp-BQY / 2-methoxyphenyl beta-D-galactopyranoside / o-methoxyphenyl beta-galactoside / OMPG / 2-methoxyphenyl beta-D-galactoside / 2-methoxyphenyl D-galactoside / 2-methoxyphenyl galactoside


Type: D-saccharide / Mass: 286.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18O7
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M ammonium sulfate, 0.1 M NaCl, 0.1 M MES pH 5.6, 32% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.25→51.26 Å / Num. obs: 83215 / % possible obs: 99.2 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Net I/σ(I): 15
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.917 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 7590 / CC1/2: 0.313 / Rpim(I) all: 1.021 / Rrim(I) all: 2.118 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AOW

6aow


Resolution: 1.25→46.896 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 3970 4.78 %
Rwork0.2083 --
obs0.209 82984 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→46.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 45 350 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042434
X-RAY DIFFRACTIONf_angle_d1.0283343
X-RAY DIFFRACTIONf_dihedral_angle_d11.887835
X-RAY DIFFRACTIONf_chiral_restr0.067388
X-RAY DIFFRACTIONf_plane_restr0.004421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26520.41861020.42352512X-RAY DIFFRACTION89
1.2652-1.28130.4471270.39542570X-RAY DIFFRACTION91
1.2813-1.29810.36061320.35642702X-RAY DIFFRACTION97
1.2981-1.31590.32031140.34152809X-RAY DIFFRACTION99
1.3159-1.33470.3261170.32222844X-RAY DIFFRACTION100
1.3347-1.35460.34861430.31052807X-RAY DIFFRACTION100
1.3546-1.37580.30731780.30722766X-RAY DIFFRACTION100
1.3758-1.39840.28261550.2852826X-RAY DIFFRACTION100
1.3984-1.42250.27771650.25912808X-RAY DIFFRACTION100
1.4225-1.44830.27361450.25922789X-RAY DIFFRACTION100
1.4483-1.47620.25281540.24382821X-RAY DIFFRACTION100
1.4762-1.50630.22241510.23622834X-RAY DIFFRACTION100
1.5063-1.53910.25961430.2382800X-RAY DIFFRACTION100
1.5391-1.57490.24481450.22112823X-RAY DIFFRACTION100
1.5749-1.61430.221330.21192846X-RAY DIFFRACTION100
1.6143-1.65790.21111560.2072825X-RAY DIFFRACTION100
1.6579-1.70670.25561370.21062865X-RAY DIFFRACTION100
1.7067-1.76180.23161470.20562836X-RAY DIFFRACTION100
1.7618-1.82480.23031230.20432849X-RAY DIFFRACTION100
1.8248-1.89780.20981430.19472862X-RAY DIFFRACTION100
1.8978-1.98420.23181440.19722839X-RAY DIFFRACTION100
1.9842-2.08880.19681100.19012895X-RAY DIFFRACTION100
2.0888-2.21970.20091750.1892839X-RAY DIFFRACTION100
2.2197-2.39110.21711580.18212871X-RAY DIFFRACTION100
2.3911-2.63170.24391270.19012889X-RAY DIFFRACTION100
2.6317-3.01240.20691600.19712921X-RAY DIFFRACTION100
3.0124-3.79510.19311260.17392950X-RAY DIFFRACTION100
3.7951-46.92940.18681600.19123016X-RAY DIFFRACTION98

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