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Yorodumi- PDB-6arm: F9 pilus adhesin FmlH lectin domain from E. coli UTI89 co-crystal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6arm | |||||||||
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Title | F9 pilus adhesin FmlH lectin domain from E. coli UTI89 co-crystallized with o-nitrophenyl beta-galactoside (ONPG) | |||||||||
Components | F9 pilus adhesin FmlH | |||||||||
Keywords | SUGAR BINDING PROTEIN / Fimbrial adhesin / lectin / bacterial adhesion | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Kalas, V. / Hultgren, S.J. | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6arm.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6arm.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 6arm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6arm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6arm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6arm_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 6arm_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/6arm ftp://data.pdbj.org/pub/pdb/validation_reports/ar/6arm | HTTPS FTP |
-Related structure data
Related structure data | 6aowSC 6aoxC 6aoyC 6arnC 6aroC 6as8C 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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2 |
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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.: 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 | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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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: 2.05 Å3/Da / Density % sol: 39.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M ammonium sulfate, 0.1M NaCl, 0.1 M MES pH 5.6, 32% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→57.3 Å / Num. obs: 46203 / % possible obs: 96 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.365 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1811 / CC1/2: 0.288 / Rpim(I) all: 0.687 / % possible all: 79.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AOW Resolution: 1.5→50 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell |
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