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Yorodumi- PDB-6maw: F9 Pilus Adhesin FmlH Lectin Domain from E. coli UTI89 in Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6maw | ||||||
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Title | F9 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 | ||||||
Components | Fimbrial adhesin FmlD | ||||||
Keywords | sugar 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 / cell adhesion Similarity search - Function | ||||||
Biological species | Escherichia coli UTI89 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Klein, R.D. / Hultgren, S.J. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6maw.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6maw.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 6maw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/6maw ftp://data.pdbj.org/pub/pdb/validation_reports/ma/6maw | HTTPS FTP |
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-Related structure data
Related structure data | 6mapC 6maqC 6aowS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: 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 |
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#2: Chemical | ChemComp-JC7 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.25 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.7 M LiSO4, 20% PEG 8000, 10% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Mar 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→37.138 Å
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Refine LS restraints |
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LS refinement shell |
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