+Open data
-Basic information
Entry | Database: PDB / ID: 2w0o | ||||||
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Title | Horse spleen apoferritin | ||||||
Components | FERRITIN LIGHT CHAIN | ||||||
Keywords | METAL TRANSPORT / IRON / ACETYLATION / APOFERRITIN / IRON STORAGE / METAL-BINDING | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | De Val, N. / Declercq, J.P. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2012 Title: Structural Analysis of Haemin Demetallation by L-Chain Apoferritins Authors: De Val, N. / Declercq, J.P. / Lim, C.K. / Crichton, R.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w0o.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w0o.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 2w0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w0o_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
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Full document | 2w0o_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 2w0o_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 2w0o_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/2w0o ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w0o | HTTPS FTP |
-Related structure data
Related structure data | 2v2iSC 2v2jC 2v2lC 2v2mC 2v2nC 2v2oC 2v2pC 2v2rC 2v2sC 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: 19872.428 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-175 / Source method: isolated from a natural source / Source: (natural) EQUUS CABALLUS (horse) / Organ: SPLEEN / References: UniProt: P02791 | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-CD / #4: 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: 60.4 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: RESERVOIR: CADMIUM SULFATE 0.12M, AMMONIUM SULFATE 0.8M, SODIUM ACETATE BUFFER 0.1M PH 5.6, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1 UL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 20, 2008 / Details: SECOND CRYSTAL SAGITALLY BENT |
Radiation | Monochromator: FIRST CRYSTAL FLAT AND N2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→22 Å / Num. obs: 77238 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.5→1.75 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.6 / % possible all: 98.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V2I Resolution: 1.5→104.83 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.124 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HORSE SPLEEN APOFERRITIN HAS BEEN PREPARED BY A METHOD WHICH RETAINS THE COFACTOR
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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: 22.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→104.83 Å
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Refine LS restraints |
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