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Yorodumi- PDB-5d8o: 1.90A resolution structure of BfrB (wild-type, C2221 form) from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d8o | ||||||
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Title | 1.90A resolution structure of BfrB (wild-type, C2221 form) from Pseudomonas aeruginosa | ||||||
Components | Ferroxidase | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / iron binding / iron mobilization | ||||||
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: 1.9 Å | ||||||
Authors | Lovell, S. / Battaile, K.P. / Wang, Y. / Yao, H. / Rivera, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2015 Title: Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein-Protein Interaction in Solution and Determination of Binding Energy Hot Spots. Authors: Wang, Y. / Yao, H. / Cheng, Y. / Lovell, S. / Battaile, K.P. / Midaugh, C.R. / Rivera, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d8o.cif.gz | 442.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d8o.ent.gz | 360.9 KB | Display | PDB format |
PDBx/mmJSON format | 5d8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d8o_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 5d8o_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 5d8o_validation.xml.gz | 90.3 KB | Display | |
Data in CIF | 5d8o_validation.cif.gz | 127.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/5d8o ftp://data.pdbj.org/pub/pdb/validation_reports/d8/5d8o | HTTPS FTP |
-Related structure data
Related structure data | 5d8pC 5d8qC 5d8rC 5d8sC 5d8xC 5d8yC 3is7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: Chemical | ChemComp-PG4 / #4: Chemical | ChemComp-HEM / #5: 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: 2.89 Å3/Da / Density % sol: 57.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 30% (v/v) PEG 200, 100 mM Na acetate, 200 sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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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 25, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→47.77 Å / Num. obs: 202062 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.91 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.6 / Num. measured all: 1371423 / Scaling rejects: 4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-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: 1.9→45.092 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 18.81 / 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: 68.47 Å2 / Biso mean: 22.2913 Å2 / Biso min: 4.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→45.092 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %
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