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Yorodumi- PDB-3is8: Structure of mineralized Bfrb soaked with FeSO4 from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3is8 | ||||||
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Title | Structure of mineralized Bfrb soaked with FeSO4 from Pseudomonas aeruginosa to 2.25A Resolution | ||||||
Components | Bacterioferritin | ||||||
Keywords | ELECTRON TRANSPORT / iron storage / Heme / Iron / Metal-binding | ||||||
Function / homology | Function and homology information 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 | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å | ||||||
Authors | Lovell, S. / Weeratunga, S.K. / Battaile, K.P. / Rivera, M. | ||||||
Citation | Journal: Biochemistry / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3is8.cif.gz | 811.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3is8.ent.gz | 670 KB | Display | PDB format |
PDBx/mmJSON format | 3is8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3is8_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 3is8_full_validation.pdf.gz | 4.3 MB | Display | |
Data in XML | 3is8_validation.xml.gz | 156.7 KB | Display | |
Data in CIF | 3is8_validation.cif.gz | 206.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/3is8 ftp://data.pdbj.org/pub/pdb/validation_reports/is/3is8 | HTTPS FTP |
-Related structure data
Related structure data | 3is7SC 3iseC 3isfC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX
#1: Protein | Mass: 18580.168 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bfrB, PA3531 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express RIL / References: UniProt: Q9HY79 |
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-Non-polymers , 5 types, 1622 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-HEM / #5: Chemical | ChemComp-SO4 / #6: 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: 2.98 Å3/Da / Density % sol: 58.67 % |
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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: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 13, 2009 |
Diffraction measurement | Details: 0.50 degrees, 9.0 sec, detector distance 200.00 mm |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.135 / Number: 1858510 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 251658 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 13.118 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.853 / Num. unique all: 24621 / Rsym value: 0.692 / % possible all: 98.5 |
Cell measurement | Reflection used: 1858510 |
-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: 2.25→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.156 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.196 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.193 / 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: 59.48 Å2 / Biso mean: 24.991 Å2 / Biso min: 4.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→50 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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