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Open data
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Basic information
Entry | Database: PDB / ID: 7dya | ||||||
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Title | Crystal structure of TmFtn with calcium ions | ||||||
![]() | Ferritin | ||||||
![]() | PROTEIN BINDING / Thermotoga maritima ferritin / Calcium ions | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Zhang, X. / Zhao, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Protein interface redesign facilitates the transformation of nanocage building blocks to 1D and 2D nanomaterials. Authors: Zhang, X. / Liu, Y. / Zheng, B. / Zang, J. / Lv, C. / Zhang, T. / Wang, H. / 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 | ![]() | 299.8 KB | Display | ![]() |
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PDB format | ![]() | 244.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4 MB | Display | ![]() |
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Full document | ![]() | 4 MB | Display | |
Data in XML | ![]() | 55.9 KB | Display | |
Data in CIF | ![]() | 81.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dy8C ![]() 7dy9C ![]() 7dybC ![]() 1vlgS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 19401.840 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1128 / Production host: ![]() ![]() #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.6 Details: 14% 2-Propanol, 70 mM Sodium acetate/ HCl pH 4.6, 140 mM Calcium chloride, 30% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.197→38.584 Å / Num. obs: 107433 / % possible obs: 99.92 % / Redundancy: 6.8 % / CC1/2: 0.992 / Net I/σ(I): 5.97 |
Reflection shell | Resolution: 2.197→2.197 Å / Num. unique obs: 10652 / CC1/2: 0.979 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VLG Resolution: 2.197→38.584 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.64 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.79 Å2 / Biso mean: 38.2521 Å2 / Biso min: 19.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.197→38.584 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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