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Yorodumi- PDB-3r2o: 1.95 A resolution structure of As-Isolated FtnA from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r2o | ||||||
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Title | 1.95 A resolution structure of As-Isolated FtnA from Pseudomonas aeruginosa (pH 6.0) | ||||||
Components | Bacterioferritin | ||||||
Keywords | METAL BINDING PROTEIN / iron binding / iron storage / iron homeostasis / iron release / iron mobilization | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Lovell, S.W. / Battaile, K.P. / Yao, H. / Jepkorir, G. / Nama, P.V. / Weeratunga, S. / Rivera, M. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Two distinct ferritin-like molecules in Pseudomonas aeruginosa: the product of the bfrA gene is a bacterial ferritin (FtnA) and not a bacterioferritin (Bfr). Authors: Yao, H. / Jepkorir, G. / Lovell, S. / Nama, P.V. / Weeratunga, S. / Battaile, K.P. / Rivera, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r2o.cif.gz | 48.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r2o.ent.gz | 34.9 KB | Display | PDB format |
PDBx/mmJSON format | 3r2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r2o_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 3r2o_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 3r2o_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 3r2o_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/3r2o ftp://data.pdbj.org/pub/pdb/validation_reports/r2/3r2o | HTTPS FTP |
-Related structure data
Related structure data | 3r2hSC 3r2kC 3r2lC 3r2mC 3r2rC 3r2sC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17964.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: bfr, bfrA, PA4235 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q9HWF9 | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: 35% (v/v) 2-methyl-2,4-pentanediol, 100 mM MES, 200 mM Li2SO4, pH 6.0, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.7401 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.7401 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→98.92 Å / Num. all: 16285 / Num. obs: 16285 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 36.55 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 30.1954 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 3R2H Resolution: 1.95→98.92 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.918 Å2 / ksol: 0.477 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.96 Å2 / Biso mean: 34.1624 Å2 / Biso min: 19.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→98.92 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: 6 / % reflection obs: 100 %
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