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Open data
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Basic information
Entry | Database: PDB / ID: 7x9z | ||||||
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Title | Thermotoga maritima ferritin variant-Tm-E(G40E) with Co | ||||||
![]() | Ferritin | ||||||
![]() | METAL BINDING PROTEIN / protein assembly | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Yu, L. / Guanghua, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Thermotoga maritima ferritin variant-Tm-E(G40E) with Co Authors: Yu, L. / Guanghua, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.4 KB | Display | ![]() |
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PDB format | ![]() | 55 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.4 KB | Display | ![]() |
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Full document | ![]() | 435.6 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 16.3 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 | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17506.645 Da / Num. of mol.: 2 / Mutation: G40E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CO / #3: 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: 2.33 Å3/Da / Density % sol: 47.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25mM HEPES, pH 8.0, 55% MPD, 5mM Cobalt chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.597735 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→53.34 Å / Num. obs: 29843 / % possible obs: 98.61 % / Redundancy: 2 % / CC1/2: 0.991 / Net I/σ(I): 13.89 |
Reflection shell | Resolution: 2.29→2.372 Å / Num. unique obs: 2470 / CC1/2: 0.976 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VLG Resolution: 2.29→53.34 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.44 / 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: 89.5 Å2 / Biso mean: 23.5665 Å2 / Biso min: 8.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.29→53.34 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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