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- PDB-7k5e: 1.75 A resolution structure of WT BfrB from Pseudomonas aeruginos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7k5e | ||||||
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Title | 1.75 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor JAG-5-7 | ||||||
![]() | Ferroxidase | ||||||
![]() | OXIDOREDUCTASE / BIOFILMS / ELECTRON TRANSPORT / IRON STORAGE / IRON BINDING / IRON MOBILIZATION / PROTEIN-PROTEIN INTERACTION INHIBITOR | ||||||
Function / homology | ![]() ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / iron ion binding / heme binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lovell, S. / Battaile, K.P. / Soldano, A. / Punchi-Hewage, A. / Meraz, K. / Annor-Gyamfi, J.K. / Yao, H. / Bunce, R.A. / Rivera, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Small Molecule Inhibitors of the Bacterioferritin (BfrB)-Ferredoxin (Bfd) Complex Kill Biofilm-Embedded Pseudomonas aeruginosa Cells. Authors: Soldano, A. / Yao, H. / Punchi Hewage, A.N.D. / Meraz, K. / Annor-Gyamfi, J.K. / Bunce, R.A. / Battaile, K.P. / Lovell, S. / Rivera, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 424.6 KB | Display | ![]() |
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PDB format | ![]() | 346.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.7 MB | Display | ![]() |
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Full document | ![]() | 5.7 MB | Display | |
Data in XML | ![]() | 85.1 KB | Display | |
Data in CIF | ![]() | 116.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k5fC ![]() 7k5gC ![]() 7k5hC ![]() 5d8oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 18580.168 Da / Num. of mol.: 12 / Fragment: BFRB Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-VXM / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.19 % / Mosaicity: 0.06 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 30% (v/v) PEG 200, 0.1M sodium acetate, 0.1M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2019 | ||||||||||||||||||||||||
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→48.57 Å / Num. obs: 256167 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.1 / Num. measured all: 1740410 / Scaling rejects: 8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5D8O Resolution: 1.75→41.36 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 24.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.31 Å2 / Biso mean: 27.7414 Å2 / Biso min: 12.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→41.36 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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