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Open data
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Basic information
Entry | Database: PDB / ID: 6ls3 | ||||||
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Title | cubic-shaped crystal of TmFtn mutant-T4FY stimulated by Mg | ||||||
![]() | Ferritin | ||||||
![]() | METAL BINDING PROTEIN / Mg | ||||||
Function / homology | ![]() bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, G. / Zhang, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: cubic-shaped crystal of TmFtn mutant-T4FY stimulated by Mg Authors: Zhao, G. / Zhang, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 274.2 KB | Display | ![]() |
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PDB format | ![]() | 223.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1vlgS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19407.887 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM Potassium phosphate monobasic, Sodium phosphate dibasic pH 6.2, and 2500 mM Sodium chloride, 60 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 273 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.815→138.703 Å / Num. obs: 50424 / % possible obs: 95 % / Redundancy: 5 % / Biso Wilson estimate: 76.05 Å2 / CC1/2: 0.999 / Net I/σ(I): 4.64 |
Reflection shell | Resolution: 2.815→2.961 Å / Num. unique obs: 5252 / CC1/2: 0.999 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VLG Resolution: 2.815→138.703 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.8 Å2 / Biso mean: 67.876 Å2 / Biso min: 35.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.815→138.703 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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