+Open data
-Basic information
Entry | Database: PDB / ID: 7x9x | ||||||
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Title | Thermotoga Maritima ferritin variant-Tm-E(G40E) with Zn | ||||||
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: 2.3 Å | ||||||
Authors | Liu, Y. / Zhao, G. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Nano / Year: 2022 Title: Directed Self-Assembly of Dimeric Building Blocks into Networklike Protein Origami to Construct Hydrogels. Authors: Liu, Y. / Chen, X. / Yin, S. / Chang, X. / Lv, C. / Zang, J. / Leng, X. / Zhang, T. / Zhao, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x9x.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x9x.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 7x9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/7x9x ftp://data.pdbj.org/pub/pdb/validation_reports/x9/7x9x | HTTPS FTP |
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-Related structure data
Related structure data | 7xa2C 7xa4C 1vlgS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 17506.645 Da / Num. of mol.: 2 / Mutation: G40E 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 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-FE / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25mM HEPES pH 8.0, 35% MPD, 2mM Zinc chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1.276911 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.276911 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→28.56 Å / Num. obs: 31502 / % possible obs: 99.69 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.3→2.382 Å / Num. unique obs: 3042 / CC1/2: 0.699 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VLG Resolution: 2.3→28.56 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.17 / 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: 134.16 Å2 / Biso mean: 40.5182 Å2 / Biso min: 17.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→28.56 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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