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Yorodumi- PDB-2cn6: Recombinant human H ferritin, K86Q and E107D mutant, soaked with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cn6 | ||||||
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Title | Recombinant human H ferritin, K86Q and E107D mutant, soaked with Zn ions | ||||||
Components | FERRITIN HEAVY CHAIN | ||||||
Keywords | OXIDOREDUCTASE / IRON / APOFERRITIN / FERROXIDASE / IRON STORAGE / METAL-BINDING / PHOSPHORYLATION / DI-IRON NON-HEME PROTEIN | ||||||
Function / homology | Function and homology information iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / 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: 2.2 Å | ||||||
Authors | Toussaint, L. / Crichton, R.R. / Declercq, J.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: High-Resolution X-Ray Structures of Human Apoferritin H-Chain Mutants Correlated with Their Activity and Metal-Binding Sites. Authors: Toussaint, L. / Bertrand, L. / Hue, L. / Crichton, R.R. / Declercq, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cn6.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cn6.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 2cn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/2cn6 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/2cn6 | HTTPS FTP |
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-Related structure data
Related structure data | 2ceiC 2chiSC 2cihC 2cluC 2cn7C 2iu2C C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21240.578 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M5219 / References: UniProt: P02794, ferroxidase | ||||||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Compound details | STORES IRON IN A SOLUBLE, NONTOXIC, READILY AVAILABLE FORM. IMPORTANT FOR IRON HOMEOSTASIS. HAS ...STORES IRON IN A SOLUBLE, NONTOXIC, READILY AVAILABLE FORM. IMPORTANT FOR IRON HOMEOSTASI | Sequence details | MUTATION K86Q, E107D | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: HANGING DROP. RESERVOIR: MPD 5% CACL2 4.7 MM, TRIS 50 MM PH 8.5 DROP: 1 UL PROTEIN (22 MG/ML) AND 1 UL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979661 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 18, 2005 / Details: TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING |
Radiation | Monochromator: FIRST CRYSTAL FLAT AND N2 COOLED. SECOND CRYSTAL SAGITTALY BENT Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979661 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→44.61 Å / Num. obs: 12895 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 23 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 23 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 2CHI Resolution: 2.2→103.14 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.261 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→103.14 Å
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Refine LS restraints |
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