+Open data
-Basic information
Entry | Database: PDB / ID: 8usm | ||||||
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Title | FmlH Lectin Domain UTI89 - AM4085 | ||||||
Components | Fimbrial protein (Fragment) | ||||||
Keywords | CELL ADHESION / Adhesin Inhibitor | ||||||
Function / homology | FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / : / Fimbrial protein Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Tamadonfar, K.O. / Pinkner, J.P. / Maddirala, A.R. / Janetka, J.W. / Hultgren, S.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8usm.cif.gz | 180.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8usm.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 8usm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/8usm ftp://data.pdbj.org/pub/pdb/validation_reports/us/8usm | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | Mass: 459.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21F4NO6 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.01 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.7 M LiSO4 2% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.976 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→38.47 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→38.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.688 Å
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Refinement TLS params. | Method: refined / Origin x: 7.4945 Å / Origin y: 13.48 Å / Origin z: 6.8714 Å
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Refinement TLS group | Selection details: all |