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Yorodumi- PDB-2v2n: Mutant R59M recombinant horse spleen apoferritin cocrystallized w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2n | ||||||
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Title | Mutant R59M recombinant horse spleen apoferritin cocrystallized with haemin in acidic conditions | ||||||
Components | FERRITIN LIGHT CHAIN | ||||||
Keywords | METAL TRANSPORT / IRON / 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: 1.55 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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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v2n.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v2n.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 2v2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v2n_validation.pdf.gz | 450.6 KB | Display | wwPDB validaton report |
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Full document | 2v2n_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 2v2n_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 2v2n_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2n ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2n | HTTPS FTP |
-Related structure data
Related structure data | 2v2iSC 2v2jC 2v2lC 2v2mC 2v2oC 2v2pC 2v2rC 2v2sC 2w0oC 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: 19830.387 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) EQUUS CABALLUS (horse) / Organ: SPLEEN / Plasmid: PMK2100 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BMH-71-18 / References: UniProt: P02791 | ||||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-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: 60.8 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: RESERVOIR: CADMIUM SULFATE 0.12M, AMMONIUM SULFATE 1.1M, SODIUM ACETATE 0.1M PH 5.6, SODIUM AZIDE 0.003M DROP: 1UL PROTEIN AND 1UL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 16, 2006 / Details: MIRROR 2 BENT, VERTICALLY FOCUSSING |
Radiation | Monochromator: SI 111, HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→12 Å / Num. obs: 36531 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.55→1.6 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.5 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V2I Resolution: 1.55→104.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.341 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.076 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→104.83 Å
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Refine LS restraints |
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