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- PDB-4toe: 2.20A resolution structure of Iron Bound BfrB (D34F) from Pseudom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4toe | ||||||
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Title | 2.20A resolution structure of Iron Bound BfrB (D34F) from Pseudomonas aeruginosa | ||||||
![]() | Bacterioferritin | ||||||
![]() | 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. / Yao, H. / Kumar, R. / Eshelman, K. / Rivera, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Authors: Yao, H. / Rui, H. / Kumar, R. / Eshelman, K. / Lovell, S. / Battaile, K.P. / Im, W. / 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 | ![]() | 827.2 KB | Display | ![]() |
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PDB format | ![]() | 682.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.5 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 149.4 KB | Display | |
Data in CIF | ![]() | 206.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4to9C ![]() 4toaC ![]() 4tobC ![]() 4tocC ![]() 4todC ![]() 4tofC ![]() 4togC ![]() 4tohC ![]() 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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Details | The asymmetric unit contains one biological unit |
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Components
-Protein , 1 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX
#1: Protein | Mass: 18612.254 Da / Num. of mol.: 24 / Mutation: D34F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 2448 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Colour: Red Prism / Density Matthews: 2.96 Å3/Da / Density % sol: 58.46 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 35% (v/v) MPD, 0.1M MES, 0.2M Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2011 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.73769 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.2→49.39 Å / Num. obs: 257692 / % possible obs: 96.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 21.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Net I/σ(I): 18.1 / Num. measured all: 1490791 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IS7 Resolution: 2.2→48.39 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 18.11 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED IN REFINEMENT
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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: 80.48 Å2 / Biso mean: 24.7504 Å2 / Biso min: 10.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→48.39 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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