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Yorodumi- PDB-6h6t: Binary crystal structure of positively and negatively supercharge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h6t | ||||||
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Title | Binary crystal structure of positively and negatively supercharged variants Ftn(pos) and Ftn(neg) from human heavy chain ferritin (propandiol condition, coordination number 8) | ||||||
Components | (Ferritin heavy ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / PROTEIN DESIGN / PROTEIN ENGINEERING / CHARGED PROTEIN CONTAINERS / BINARY PROTEIN STRUCTURES / SELF-ASSEMBLY / BINARY NANOPARTICLE SUPERLATTICES | ||||||
Function / homology | Function and homology information iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / Iron uptake and transport / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kuenzle, M. / Lach, M. / Beck, T. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Self-assembly of protein crystals into different crystal structures using charged patches on oppositely charged ferritin protein containers Authors: Kuenzle, M. / Lach, M. / Beck, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h6t.cif.gz | 430.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h6t.ent.gz | 353 KB | Display | PDB format |
PDBx/mmJSON format | 6h6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/6h6t ftp://data.pdbj.org/pub/pdb/validation_reports/h6/6h6t | HTTPS FTP |
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-Related structure data
Related structure data | 6h6uC 2ceiS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Ferritin heavy ... , 2 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 21499.246 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase #2: Protein | Mass: 21355.549 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase |
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-Non-polymers , 6 types, 562 molecules
#3: Chemical | ChemComp-FE / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ZN / #7: Chemical | ChemComp-CL / #8: 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: 3.18 Å3/Da / Density % sol: 61.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 100 mM sodium acetate pH 4.5, 42 % propanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.46 Å / Num. obs: 244878 / % possible obs: 99.5 % / Redundancy: 4.22 % / Rmerge(I) obs: 0.0738 / Rrim(I) all: 0.0844 / Net I/σ(I): 14.75 |
Reflection shell | Resolution: 1.9→2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CEI Resolution: 1.9→48.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.239 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.119 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.89 Å2 / Biso mean: 27.276 Å2 / Biso min: 10.16 Å2
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Refinement step | Cycle: final / Resolution: 1.9→48.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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