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- PDB-5d8p: 2.35A resolution structure of iron bound BfrB (wild-type, C2221 f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d8p | ||||||
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Title | 2.35A resolution structure of iron bound BfrB (wild-type, C2221 form) 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 | ![]() | 414.5 KB | Display | ![]() |
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PDB format | ![]() | 336 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5d8oC ![]() 5d8qC ![]() 5d8rC ![]() 5d8sC ![]() 5d8xC ![]() 5d8yC ![]() 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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1 | ![]()
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: T (tetrahedral)) | |||||||||
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.) ![]() Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: bfrB, PA3531 / Plasmid: pET11a / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 601 molecules ![](data/chem/img/K.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-FE2 / #4: Chemical | ChemComp-HEM / #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.92 % |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||
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: 2.35→49.02 Å / Num. obs: 108455 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.064 / Net I/σ(I): 11.6 / Num. measured all: 706154 | |||||||||||||||||||||||||||
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: 2.35→49.019 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.03 / 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: 110.19 Å2 / Biso mean: 39.214 Å2 / Biso min: 18.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→49.019 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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