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Yorodumi- PDB-6nlk: 1.85 A resolution structure of WT BfrB from Pseudomonas aeruginos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nlk | ||||||||||||
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Title | 1.85 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor (analog 13) | ||||||||||||
Components | Ferroxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / IRON BINDING / IRON MOBILIZATION / PROTEIN-PROTEIN INTERACTION INHIBITOR | ||||||||||||
Function / homology | Function and homology information 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 | Pseudomonas aeruginosa (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||||||||
Authors | Lovell, S. / Punchi-Hewage, A. / Battaile, K.P. / Yao, H. / Nammalwar, B. / Gnanasekaran, K.K. / Bunce, R.A. / Reitz, A.B. / Rivera, M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Small Molecule Inhibitors of the BfrB-Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity. Authors: Punchi Hewage, A.N.D. / Yao, H. / Nammalwar, B. / Gnanasekaran, K.K. / Lovell, S. / Bunce, R.A. / Eshelman, K. / Phaniraj, S.M. / Lee, M.M. / Peterson, B.R. / Battaile, K.P. / Reitz, A.B. / Rivera, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nlk.cif.gz | 435.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nlk.ent.gz | 355.2 KB | Display | PDB format |
PDBx/mmJSON format | 6nlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nlk_validation.pdf.gz | 5.5 MB | Display | wwPDB validaton report |
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Full document | 6nlk_full_validation.pdf.gz | 5.4 MB | Display | |
Data in XML | 6nlk_validation.xml.gz | 86.6 KB | Display | |
Data in CIF | 6nlk_validation.cif.gz | 118.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/6nlk ftp://data.pdbj.org/pub/pdb/validation_reports/nl/6nlk | HTTPS FTP |
-Related structure data
Related structure data | 6nlfC 6nlgC 6nliC 6nljC 6nllC 6nlmC 6nlnC 5d8oS 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
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 18580.168 Da / Num. of mol.: 12 / Fragment: BFRB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: bfrB, PA3531 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS RIL / References: UniProt: Q9HY79, ferroxidase |
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-Non-polymers , 5 types, 1559 molecules
#2: Chemical | #3: Chemical | ChemComp-KTG / #4: Chemical | ChemComp-HEM / #5: Chemical | ChemComp-PG4 / #6: 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: 2.88 Å3/Da / Density % sol: 57.31 % / Mosaicity: 0.07 ° |
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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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.64 Å / Num. obs: 216954 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.3 / Num. measured all: 1479771 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.956 / Num. unique obs: 10635 / CC1/2: 0.779 / % possible all: 99.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D8O Resolution: 1.85→47.307 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 20.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.13 Å2 / Biso mean: 26.5251 Å2 / Biso min: 7.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→47.307 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
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