+Open data
-Basic information
Entry | Database: PDB / ID: 5wpn | ||||||
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Title | Zn-bound Structure of Chaetopterus variopedatus Ferritin | ||||||
Components | Ferritin | ||||||
Keywords | OXIDOREDUCTASE / Ferritin | ||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm Similarity search - Function | ||||||
Biological species | Chaetopterus variopedatus (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | De Meulenaere, E. / Bailey, J.B. / Tezcan, F.A. / Deheyn, D. | ||||||
Citation | Journal: Biochem. J. / Year: 2017 Title: First biochemical and crystallographic characterization of a fast-performing ferritin from a marine invertebrate. Authors: De Meulenaere, E. / Bailey, J.B. / Tezcan, F.A. / Deheyn, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wpn.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wpn.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wpn_validation.pdf.gz | 442.6 KB | Display | wwPDB validaton report |
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Full document | 5wpn_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 5wpn_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 5wpn_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/5wpn ftp://data.pdbj.org/pub/pdb/validation_reports/wp/5wpn | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | 24-meric cage-like protein by gel filtration |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19824.100 Da / Num. of mol.: 1 / Mutation: N82D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetopterus variopedatus (invertebrata) Production host: Escherichia coli (E. coli) / References: UniProt: A0A075ML49, ferroxidase |
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-Non-polymers , 6 types, 305 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: 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: 3.19 Å3/Da / Density % sol: 61.4 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: Reservoir: 500 uL total volume: 20 mM Tris (pH 8.5), 40 mM CaCl2, 6% PEG 400 Sitting Drop: 2 uL reservoir, 2 uL of 25 uM Chaetopterus variopedatus ferritin Soaking Solution (30 min): 10 mM ...Details: Reservoir: 500 uL total volume: 20 mM Tris (pH 8.5), 40 mM CaCl2, 6% PEG 400 Sitting Drop: 2 uL reservoir, 2 uL of 25 uM Chaetopterus variopedatus ferritin Soaking Solution (30 min): 10 mM Zn, 20 mM Tris (pH 8.5), 20 mM CaCl2, and 3% (v/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.97946 |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→90.94 Å / Num. obs: 36446 / % possible obs: 99.9 % / Redundancy: 25.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.095 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 296 / CC1/2: 0.568 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: homology model Resolution: 1.57→45.467 Å / Cross valid method: THROUGHOUT
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→45.467 Å
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LS refinement shell | Resolution: 1.57→1.61 Å /
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