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- PDB-8usm: FmlH Lectin Domain UTI89 - AM4085 -

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Basic information

Entry
Database: PDB / ID: 8usm
TitleFmlH Lectin Domain UTI89 - AM4085
ComponentsFimbrial protein (Fragment)
KeywordsCELL ADHESION / Adhesin Inhibitor
Function / homologyFimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / : / Fimbrial protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsTamadonfar, K.O. / Pinkner, J.P. / Maddirala, A.R. / Janetka, J.W. / 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)R01DK10884 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery of Orally Bioavailable FmlH Lectin Antagonists as Treatment for Urinary Tract Infections.
Authors: Maddirala, A.R. / Tamadonfar, K. / Pinkner, J.S. / Sanick, D. / Hultgren, S.J. / Janetka, J.W.
History
DepositionOct 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fimbrial protein (Fragment)
B: Fimbrial protein (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7594
Polymers35,8402
Non-polymers9192
Water1,29772
1
A: Fimbrial protein (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3792
Polymers17,9201
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fimbrial protein (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3792
Polymers17,9201
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.245, 116.450, 50.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Fimbrial protein (Fragment)


Mass: 17920.088 Da / Num. of mol.: 2 / Fragment: Lectin Domain UTI89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: G3W53_27805 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T6QH46
#2: Chemical ChemComp-XC8 / 4'-fluoro-6-(trifluoromethyl)[1,1'-biphenyl]-2-yl 2-acetamido-2-deoxy-beta-D-galactopyranoside


Mass: 459.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21F4NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.7 M LiSO4 2% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.976 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.63→38.47 Å / Num. obs: 38858 / % possible obs: 99.57 % / Redundancy: 7.1 % / Biso Wilson estimate: 15.11 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05884 / Rpim(I) all: 0.02366 / Rrim(I) all: 0.06349 / Net I/σ(I): 22.76
Reflection shellResolution: 1.63→1.688 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.3694 / Mean I/σ(I) obs: 4.89 / Num. unique obs: 3807 / CC1/2: 0.951 / CC star: 0.987 / Rpim(I) all: 0.1463 / Rrim(I) all: 0.3977 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→38.47 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 2007 -
Rwork0.2024 --
obs-38858 99.57 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 64 72 2447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052441
X-RAY DIFFRACTIONf_angle_d0.9083352
X-RAY DIFFRACTIONf_dihedral_angle_d9.7131370
X-RAY DIFFRACTIONf_chiral_restr0.052381
X-RAY DIFFRACTIONf_plane_restr0.005420
LS refinement shellResolution: 1.63→1.688 Å
RfactorNum. reflection% reflection
Rfree0.2527 187 -
Rwork0.2017 3807 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 7.4945 Å / Origin y: 13.48 Å / Origin z: 6.8714 Å
111213212223313233
T0.1143 Å20.0113 Å2-0.0001 Å2-0.0959 Å20.0134 Å2--0.1001 Å2
L1.2263 °2-0.2123 °20.0389 °2-0.5384 °2-0.0504 °2--0.0432 °2
S-0.0446 Å °-0.0384 Å °0.0494 Å °0.0385 Å °0.0396 Å °0.0032 Å °-0.0421 Å °-0.0188 Å °-0.0015 Å °
Refinement TLS groupSelection details: all

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