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- PDB-6maw: F9 Pilus Adhesin FmlH Lectin Domain from E. coli UTI89 in Complex... -

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Basic information

Entry
Database: PDB / ID: 6maw
TitleF9 Pilus Adhesin FmlH Lectin Domain from E. coli UTI89 in Complex with Galactoside N-[(2S,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[S-methyl-6-(trifluoromethyl)-[1,1'-biphenyl]-3'-yl]oxy}oxan-3-yl]acetamide
ComponentsFimbrial adhesin FmlD
Keywordssugar binding protein/inhibitor / Pilus / Adhesin / Galactose / Lectin / SUGAR BINDING PROTEIN / sugar binding protein-inhibitor complex
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus
Similarity search - Function
Fimbrial-type adhesion domain / FimH, mannose-binding domain / FimH, mannose binding / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-JC7 / Fimbrial adhesin / Uncharacterized fimbrial-like protein YdeQ
Similarity search - Component
Biological speciesEscherichia coli UTI89 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKlein, R.D. / Hultgren, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI048689 United States
Citation
Journal: J.Med.Chem. / Year: 2019
Title: Biphenyl Gal and GalNAc FmlH Lectin Antagonists of Uropathogenic E. coli (UPEC): Optimization through Iterative Rational Drug Design.
Authors: Maddirala, A.R. / Klein, R. / Pinkner, J.S. / Kalas, V. / Hultgren, S.J. / Janetka, J.W.
#1: Journal: To Be Published
Title: Development of Novel FmlH Inhibitors to Treat Chronic Cystitis
Authors: Klein, R.D. / Hultgren, S.J.
History
DepositionAug 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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 1.3Dec 13, 2023Group: 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 1.4Nov 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: Fimbrial adhesin FmlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4552
Polymers17,9201
Non-polymers5351
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.445, 110.212, 90.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-446-

HOH

21A-511-

HOH

31A-569-

HOH

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Components

#1: Protein Fimbrial adhesin FmlD / Fimbrial protein / Fimbrial-like protein YdeQ / Fml fimbrial adhesin FmlD / Putative adhesin ...Fimbrial protein / Fimbrial-like protein YdeQ / Fml fimbrial adhesin FmlD / Putative adhesin similar to FimH protein


Mass: 17920.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli UTI89 (bacteria) / Strain: UTI89
Gene: b1502, fmlD, ydeQ, AC789_1c16310, ACN002_1542, B1K96_25685, BK292_08390, BN17_21261, C7B02_22960, CR538_13120, CWS33_06125, CXB56_15680, HW43_11455, RX35_00290
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: J7QR14, UniProt: P77588*PLUS
#2: Chemical ChemComp-JC7 / N-[2'-{[2-(acetylamino)-2-deoxy-beta-D-galactopyranosyl]oxy}-6'-(trifluoromethyl)[1,1'-biphenyl]-3-yl]methanesulfonamide


Mass: 534.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25F3N2O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.7 M LiSO4, 20% PEG 8000, 10% DMSO

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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: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→45.1 Å / Num. obs: 20289 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.099 / Net I/σ(I): 17.65
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 5.07 / Num. unique obs: 2088 / CC1/2: 0.941 / Rrim(I) all: 0.429 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AOW

6aow


Resolution: 1.75→37.138 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.3
RfactorNum. reflection% reflectionSelection details
Rfree0.182 986 4.86 %Random selection
Rwork0.1606 ---
obs0.1616 20289 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→37.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 36 274 1510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071286
X-RAY DIFFRACTIONf_angle_d1.1381772
X-RAY DIFFRACTIONf_dihedral_angle_d13.457450
X-RAY DIFFRACTIONf_chiral_restr0.053202
X-RAY DIFFRACTIONf_plane_restr0.005223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.84230.21161420.17682704X-RAY DIFFRACTION100
1.8423-1.95770.20551330.16932736X-RAY DIFFRACTION100
1.9577-2.10890.18631590.16022691X-RAY DIFFRACTION100
2.1089-2.32110.18181440.15282739X-RAY DIFFRACTION100
2.3211-2.65680.18721400.15872750X-RAY DIFFRACTION100
2.6568-3.3470.20151470.16372760X-RAY DIFFRACTION100
3.347-37.14640.14421210.15672923X-RAY DIFFRACTION100

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