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- PDB-5d8y: 2.05A resolution structure of iron bound BfrB (L68A E81A) from Ps... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d8y | ||||||
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Title | 2.05A resolution structure of iron bound BfrB (L68A E81A) from Pseudomonas aeruginosa | ||||||
![]() | Ferroxidase | ||||||
![]() | OXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / iron binding / iron mobilization | ||||||
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. / Wang, Y. / Yao, H. / Rivera, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 862.4 KB | Display | ![]() |
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PDB format | ![]() | 707.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 164.5 KB | Display | |
Data in CIF | ![]() | 227.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d8oC ![]() 5d8pC ![]() 5d8qC ![]() 5d8rC ![]() 5d8sC ![]() 5d8xC ![]() 3is7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX
#1: Protein | Mass: 18480.053 Da / Num. of mol.: 24 / Fragment: BfrB / Mutation: L68A, E81A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: bfrB, PA3531 / Plasmid: pET11a / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 3186 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-HEM / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30% (v/v) 2-methyl-2,4-pentanediol, 100 mM Na acetate, 20 calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
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: 2.05→48.75 Å / Num. obs: 302900 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 24.44 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.1 / Num. measured all: 1491879 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IS7 Resolution: 2.05→48.748 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.09 / 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: 106.25 Å2 / Biso mean: 27.5792 Å2 / Biso min: 11.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→48.748 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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