+Open data
-Basic information
Entry | Database: PDB / ID: 4de6 | ||||||
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Title | Horse spleen apo-ferritin complex with arachidonic acid | ||||||
Components | Ferritin light chain | ||||||
Keywords | TRANSPORT PROTEIN / four helix bundle | ||||||
Function / homology | Function and homology information : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Bu, W. / Liu, R. / Dmochowski, I.J. / Loll, P.J. / Eckenhoff, R.G. | ||||||
Citation | Journal: Faseb J. / Year: 2012 Title: Ferritin couples iron and fatty acid metabolism. Authors: Bu, W. / Liu, R. / Cheung-Lau, J.C. / Dmochowski, I.J. / Loll, P.J. / Eckenhoff, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4de6.cif.gz | 53.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4de6.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 4de6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4de6_validation.pdf.gz | 753.1 KB | Display | wwPDB validaton report |
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Full document | 4de6_full_validation.pdf.gz | 754.8 KB | Display | |
Data in XML | 4de6_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 4de6_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/4de6 ftp://data.pdbj.org/pub/pdb/validation_reports/de/4de6 | HTTPS FTP |
-Related structure data
Related structure data | 1xz1S 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: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791 | ||||
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#2: Chemical | ChemComp-ACD / | ||||
#3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: (NH4)2SO4 and CDSO4, ,0.2 mM arachidonate was mixed in the reservoir, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 23, 2011 |
Radiation | Monochromator: VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→25.32 Å / Num. all: 15560 / Num. obs: 12950 / % possible obs: 0.99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4.8 / Redundancy: 20.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.18→2.25 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.8 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1XZ1 Resolution: 2.18→25.32 Å / SU ML: 0.17 / σ(F): 0.35 / Phase error: 20.78 / 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 / Bsol: 32.549 Å2 / ksol: 0.405 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.18→25.32 Å
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Refine LS restraints |
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LS refinement shell |
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