+Open data
-Basic information
Entry | Database: PDB / ID: 3rgd | ||||||
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Title | Iron loaded frog M ferritin. Short soaking time | ||||||
Components | Ferritin, middle subunit | ||||||
Keywords | OXIDOREDUCTASE / eukaryotic ferritin / four-helix bundle / ferroxidase | ||||||
Function / homology | Function and homology information ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm Similarity search - Function | ||||||
Biological species | Rana catesbeiana (American bullfrog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Bertini, I. / Lalli, D. / Mangani, S. / Pozzi, C. / Rosa, C. / Theil, E.C. / Turano, P. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: Structural insights into the ferroxidase site of ferritins from higher eukaryotes. Authors: Bertini, I. / Lalli, D. / Mangani, S. / Pozzi, C. / Rosa, C. / Theil, E.C. / Turano, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rgd.cif.gz | 827.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rgd.ent.gz | 692 KB | Display | PDB format |
PDBx/mmJSON format | 3rgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/3rgd ftp://data.pdbj.org/pub/pdb/validation_reports/rg/3rgd | HTTPS FTP |
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-Related structure data
Related structure data | 3rbcSC 3re7C 4dasC 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
#1: Protein | Mass: 20623.182 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Production host: Escherichia coli (E. coli) / References: UniProt: P07798, ferroxidase #2: Chemical | ChemComp-FE / #3: 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: 4.17 Å3/Da / Density % sol: 70.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 7 mg/mL frog M ferritin solution at pH 7.5 with TrisHCl. Precipitant: 2.1M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.74 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2010 |
Radiation | Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.74 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→50.01 Å / Num. all: 184115 / Num. obs: 184115 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 43.26 Å2 / Rsym value: 0.129 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 2.89→3.05 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 3.8 / Num. unique all: 26736 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3RBC Resolution: 2.89→48.537 Å / SU ML: 0.39 / σ(F): 1.33 / 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 / Bsol: 11.63 Å2 / ksol: 0.335 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→48.537 Å
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Refine LS restraints |
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LS refinement shell |
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