+Open data
-Basic information
Entry | Database: PDB / ID: 7xa1 | ||||||
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Title | Thermotoga maritima ferritin variant-Tm-E(S111Y) | ||||||
Components | Ferritin | ||||||
Keywords | METAL BINDING PROTEIN / protein assembly | ||||||
Function / homology | Function and homology information bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yu, L. / Guanghua, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Thermotoga maritima ferritin variant-Tm-E(S111Y) Authors: Yu, L. / Guanghua, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xa1.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xa1.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/7xa1 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/7xa1 | 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 | Similarity search - Function & homologyF&H Search |
-Links
-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: 17510.680 Da / Num. of mol.: 1 / Mutation: S111Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25mM HEPES pH 7.5, 35% 1,4-dioxane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.276911 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.276911 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→27.64 Å / Num. obs: 12639 / % possible obs: 91.55 % / Redundancy: 1.1 % / CC1/2: 1 / Net I/σ(I): 7.44 |
Reflection shell | Resolution: 2.2→2.28 Å / Num. unique obs: 649 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vlg Resolution: 2.2→27.64 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.51 / 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: 72.59 Å2 / Biso mean: 32.8462 Å2 / Biso min: 17.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→27.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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