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Yorodumi- PDB-6nlf: 1.45 A resolution structure of apo BfrB from Pseudomonas aeruginosa -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nlf | ||||||||||||
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Title | 1.45 A resolution structure of apo BfrB from Pseudomonas aeruginosa | ||||||||||||
Components | Ferroxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / IRON BINDING / IRON MOBILIZATION / PROTEIN-PROTEIN INTERACTION | ||||||||||||
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: 1.45 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 | 6nlf.cif.gz | 446 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nlf.ent.gz | 361.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nlf_validation.pdf.gz | 455.4 KB | Display | wwPDB validaton report |
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Full document | 6nlf_full_validation.pdf.gz | 458.4 KB | Display | |
Data in XML | 6nlf_validation.xml.gz | 88.7 KB | Display | |
Data in CIF | 6nlf_validation.cif.gz | 134.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/6nlf ftp://data.pdbj.org/pub/pdb/validation_reports/nl/6nlf | HTTPS FTP |
-Related structure data
Related structure data | 6nlgC 6nliC 6nljC 6nlkC 6nllC 6nlmC 6nlnC 3is7S 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: 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 #2: Chemical | #3: 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: 2.94 Å3/Da / Density % sol: 58.13 % / Mosaicity: 0.09 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 8% (w/v) PEG 8000, 0.1 M sodium acetate |
-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: Jul 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→47.9 Å / Num. obs: 458281 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.8 / Num. measured all: 2993762 / Scaling rejects: 3 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.901 / Num. unique obs: 22670 / CC1/2: 0.7 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IS7 Resolution: 1.45→37.177 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 14.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.69 Å2 / Biso mean: 17.4653 Å2 / Biso min: 6.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→37.177 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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