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- PDB-7dl5: Crystal structure of Thermotoga Maritima ferritin mutant at 2.3 A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dl5 | ||||||
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Title | Crystal structure of Thermotoga Maritima ferritin mutant at 2.3 Angstrom resolution | ||||||
![]() | Ferritin | ||||||
![]() | METAL BINDING PROTEIN | ||||||
Function / homology | ![]() bacterial non-heme ferritin / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Leng, X. / Zang, J. / Zhao, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A short helix regulates conversion of dimeric and 24-meric ferritin architectures. Authors: Liu, Y. / Zang, J. / Leng, X. / Zhao, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.8 KB | Display | ![]() |
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PDB format | ![]() | 109.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.2 KB | Display | ![]() |
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Full document | ![]() | 433.4 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17303.385 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: Tmari_1134 / Production host: ![]() ![]() #2: Chemical | #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: 3.56 Å3/Da / Density % sol: 65.48 % |
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Crystal grow | Temperature: 293.2 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 6.5 1.6M Magnesium Sulfate Hexahydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.61 Å / Num. obs: 20913 / % possible obs: 99.68 % / Redundancy: 2.5 % / Biso Wilson estimate: 38.22 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.3→2.384 Å / Num. unique obs: 2059 / CC1/2: 0.99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VLG Resolution: 2.3→29.61 Å / SU ML: 0.2783 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 23.5291 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.61 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -27.4052487341 Å / Origin y: -14.7261557493 Å / Origin z: 36.4947159836 Å
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Refinement TLS group | Selection details: all |