+Open data
-Basic information
Entry | Database: PDB / ID: 7dy9 | ||||||
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Title | Thermotoga maritima ferritin mutant-FLAL | ||||||
Components | Ferritin | ||||||
Keywords | RECOMBINATION / Thermotoga maritima ferritin / mutant | ||||||
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: 2.303 Å | ||||||
Authors | Zhao, G. / Zhang, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dy9.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dy9.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/7dy9 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/7dy9 | HTTPS FTP |
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-Related structure data
Related structure data | 7dy8C 7dyaC 7dybC 1vlgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19344.898 Da / Num. of mol.: 2 / Mutation: E112L, E113A, K114L, N147F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin #2: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 30% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.987 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.303→45 Å / Num. obs: 14942 / % possible obs: 95.24 % / Redundancy: 7.6 % / CC1/2: 0.997 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.303→2.64 Å / Num. unique obs: 9361 / CC1/2: 0.935 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VLG Resolution: 2.303→44.065 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 46.64 / 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: 86.56 Å2 / Biso mean: 52.5145 Å2 / Biso min: 31.01 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.303→44.065 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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