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Yorodumi- PDB-2v2o: Mutant R59M recombinant horse spleen apoferritin cocrystallized w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2o | ||||||
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Title | Mutant R59M recombinant horse spleen apoferritin cocrystallized with haemin in basic 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: 1.87 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 | 2v2o.cif.gz | 54.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v2o.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 2v2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v2o_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 2v2o_full_validation.pdf.gz | 447.1 KB | Display | |
Data in XML | 2v2o_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 2v2o_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2o ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2o | HTTPS FTP |
-Related structure data
Related structure data | 2v2iC 2v2jC 2v2lC 2v2mC 2v2nSC 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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1 |
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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 | ChemComp-GOL / | #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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE |
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Crystal grow | pH: 8.2 Details: RESERVOIR: CADMIUM SULFATE 0.145M, AMMONIUM SULFATE 0.55M, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR, pH 8.2 |
-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 1, FLAT PRE-MIRROR, 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: 1.87→21 Å / Num. obs: 22374 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.87→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.9 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V2N Resolution: 1.87→106 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.052 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.121 / 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: 15.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→106 Å
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Refine LS restraints |
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