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Yorodumi- PDB-4e6k: 2.0 A resolution structure of Pseudomonas aeruginosa bacterioferr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e6k | ||||||
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Title | 2.0 A resolution structure of Pseudomonas aeruginosa bacterioferritin (BfrB) in complex with bacterioferritin associated ferredoxin (Bfd) | ||||||
Components |
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Keywords | METAL BINDING PROTEIN/ELECTRON TRANSPORT / protein complex / iron storage / iron binding / iron mobilization / ferritin / iron homeostasis / bacterial iron metabolism / METAL BINDING PROTEIN-ELECTRON TRANSPORT complex | ||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / 2 iron, 2 sulfur cluster binding / iron ion transport / iron ion binding / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Lovell, S. / Battaile, K.P. / Yao, H. / Wang, Y. / Kumar, R. / Ruvinsky, A. / Vasker, I. / Rivera, M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: The Structure of the BfrB-Bfd Complex Reveals Protein-Protein Interactions Enabling Iron Release from Bacterioferritin. Authors: Yao, H. / Wang, Y. / Lovell, S. / Kumar, R. / Ruvinsky, A.M. / Battaile, K.P. / Vakser, I.A. / Rivera, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e6k.cif.gz | 262 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e6k.ent.gz | 211.3 KB | Display | PDB format |
PDBx/mmJSON format | 4e6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e6k_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 4e6k_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 4e6k_validation.xml.gz | 51.2 KB | Display | |
Data in CIF | 4e6k_validation.cif.gz | 74.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/4e6k ftp://data.pdbj.org/pub/pdb/validation_reports/e6/4e6k | HTTPS FTP |
-Related structure data
Related structure data | 3is7S S: Starting model for refinement |
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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 , 2 types, 9 molecules ABCDEFGHI
#1: Protein | Mass: 18580.168 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (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 #2: Protein | Mass: 7813.858 Da / Num. of mol.: 3 / Mutation: C43S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: BFD, PA3530 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS RIL / References: UniProt: Q9HY80 |
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-Non-polymers , 6 types, 1078 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / #6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: 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: 3.39 Å3/Da / Density % sol: 63.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.8 M sodium/potassium hydrogen phosphate, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-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: Feb 16, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→200.89 Å / Num. all: 125332 / Num. obs: 125332 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 3 / Num. unique all: 6150 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IS7 Resolution: 2→47.731 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.62 / Phase error: 15.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.567 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.84 Å2 / Biso mean: 23.9777 Å2 / Biso min: 8.36 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.731 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
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