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- PDB-2v2m: Mutant (E53,56,57,60Q) recombinant horse spleen apoferritin cocry... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v2m | ||||||
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Title | Mutant (E53,56,57,60Q) recombinant horse spleen apoferritin cocrystallized with haemin in basic conditions | ||||||
![]() | FERRITIN LIGHT CHAIN | ||||||
![]() | METAL TRANSPORT / IRON / HAEMIN / APOFERRITIN / IRON STORAGE / METAL-BINDING | ||||||
Function / homology | ![]() : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | De Val, N. / Declercq, J.P. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.2 KB | Display | ![]() |
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PDB format | ![]() | 40.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.6 KB | Display | ![]() |
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Full document | ![]() | 442.4 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v2iC ![]() 2v2jC ![]() 2v2lSC ![]() 2v2nC ![]() 2v2oC ![]() 2v2pC ![]() 2v2rC ![]() 2v2sC ![]() 2w0oC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 19852.445 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 53 TO GLN ENGINEERED RESIDUE IN CHAIN A, GLU 56 TO GLN ...ENGINEERED | Sequence details | MUTATIONS E53,56,57,60Q | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.4 % / Description: NONE |
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Crystal grow | pH: 8 Details: RESERVOIR: CADMIUM SULFATE 0.044M, AMMONIUM SULFATE 0.5M, SODIUM AZIDE 0.003M. DROP: 1UL PROTEIN AND 1UL RESERVOIR, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 21, 2004 / Details: RH COATED, ZERODUR, VERTICAL FOCUSSING POSSIBLE |
Radiation | Monochromator: FIXED EXIT DOUBLE CRYSTAL SI 111, HORIZONTALLY FOCUSSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.22 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→25 Å / Num. obs: 31920 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.65→1.7 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2V2L Resolution: 1.65→105.41 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.368 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / 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: 14.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→105.41 Å
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Refine LS restraints |
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