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- PDB-3is7: Structure of mineralized Bfrb from Pseudomonas aeruginosa to 2.1A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3is7 | ||||||
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Title | Structure of mineralized Bfrb from Pseudomonas aeruginosa to 2.1A Resolution | ||||||
![]() | Bacterioferritin | ||||||
![]() | ELECTRON TRANSPORT / iron storage / Heme / Iron / Metal-binding | ||||||
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. / Weeratunga, S.K. / Battaile, K.P. / Rivera, M. | ||||||
![]() | ![]() Title: Structural Studies of Bacterioferritin B from Pseudomonas aeruginosa Suggest a Gating Mechanism for Iron Uptake via the Ferroxidase Center Authors: Weeratunga, S.K. / Lovell, S. / Yao, H. / Battaile, K.P. / Fischer, C.J. / Gee, C.E. / 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 | ![]() | 769.3 KB | Display | ![]() |
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PDB format | ![]() | 637.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 153.1 KB | Display | |
Data in CIF | ![]() | 201.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3is8C ![]() 3iseC ![]() 3isfC ![]() 1bfrS 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 | biological unit is the same as asym. |
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Components
#1: Protein | Mass: 18580.168 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-K / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6 Details: 35% MPD, 100mM MES, 200mM Li2SO4, pH 6.0, vapor diffusion, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 13, 2009 |
Diffraction measurement | Details: 0.50 degrees, 9.0 sec, detector distance 180.00 mm |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.109 / Number: 2179278 |
Reflection | Resolution: 2.1→47.04 Å / Num. obs: 309226 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 16.162 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.007 / Num. unique all: 30544 / Rsym value: 0.669 / % possible all: 99.4 |
Cell measurement | Reflection used: 2179278 |
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Processing
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Refinement | Method to determine structure: MOLREP Starting model: PDB entry 1BFR Resolution: 2.1→47.04 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.552 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.11 Å2 / Biso mean: 27.328 Å2 / Biso min: 12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→47.04 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: 20
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