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Yorodumi- PDB-2cih: Recombinant human H ferritin, K86Q and E27D mutant, soaked with Zn -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cih | ||||||
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Title | Recombinant human H ferritin, K86Q and E27D mutant, soaked with Zn | ||||||
Components | FERRITIN HEAVY CHAIN | ||||||
Keywords | OXIDOREDUCTASE / APOFERRITIN / FERROXIDASE / DI-IRON NON-HEME PROTEIN / IRON STORAGE / IRON / METAL-BINDING / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information iron ion sequestering activity / : / negative regulation of ferroptosis / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation ...iron ion sequestering activity / : / negative regulation of ferroptosis / 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 uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 2cih.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cih.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 2cih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cih_validation.pdf.gz | 426.4 KB | Display | wwPDB validaton report |
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Full document | 2cih_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 2cih_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 2cih_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2cih ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2cih | HTTPS FTP |
-Related structure data
Related structure data | 2ceiC 2chiSC 2cluC 2cn6C 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21240.580 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-GOL / | #4: Water | ChemComp-HOH / | Compound details | STORES IRON IN A SOLUBLE, NONTOXIC, READILY AVAILABLE FORM ENGINEERED RESIDUE IN CHAIN A, GLU 27 TO ...STORES IRON IN A SOLUBLE, NONTOXIC, READILY AVAILABLE FORM ENGINEERED | Sequence details | MUTATION K86Q, E27D | |
-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: 7.5 Details: HANGING DROP. RESERVOIR: MPD 5% CACL2 4.7 MM, HEPES 50 MM PH 7.5 DROP: 1 UL PROTEIN (27MG/ML) AND 1 UL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.22 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 22, 2004 / Details: BENT MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL FOCUSSING MONO CHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.22 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→54.5 Å / Num. obs: 40938 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CHI Resolution: 1.5→104.26 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.956 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.064 / 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: 16.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→104.26 Å
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Refine LS restraints |
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