+Open data
-Basic information
Entry | Database: PDB / ID: 3shx | ||||||
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Title | Frog M-ferritin with magnesium, L134P mutant | ||||||
Components | Ferritin, middle subunit | ||||||
Keywords | OXIDOREDUCTASE / IRON STORAGE / DIIRON / METAL-BINDING | ||||||
Function / homology | Function and homology information ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis Similarity search - Function | ||||||
Biological species | Rana catesbeiana (American bullfrog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Tosha, T. / Ng, H.L. / Alber, T. / Theil, E.C. | ||||||
Citation | Journal: To be Published Title: Frog M-ferritin with magnesium, L134P mutant Authors: Tosha, T. / Ng, H.L. / Alber, T. / Theil, E.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3shx.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3shx.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 3shx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/3shx ftp://data.pdbj.org/pub/pdb/validation_reports/sh/3shx | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 20607.139 Da / Num. of mol.: 1 / Mutation: L134P 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 | ||||||
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#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #5: 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: 3.14 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2M MGCL2, 0.1M BICINE, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→65 Å / Num. all: 59574 / Num. obs: 59574 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8379 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→55.38 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.185 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.943 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→55.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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