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Yorodumi- PDB-2v2l: Mutant (E53,56,57,60Q) recombinant horse spleen apoferritin cocry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2l | ||||||
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Title | Mutant (E53,56,57,60Q) 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 ferritin complex / 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: 1.9 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 | 2v2l.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v2l.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 2v2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2l ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2l | HTTPS FTP |
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-Related structure data
Related structure data | 2v2iSC 2v2jC 2v2mC 2v2nC 2v2oC 2v2pC 2v2rC 2v2sC 2w0oC S: Starting model for refinement C: citing same article (ref.) |
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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: 19852.445 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-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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.2 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: RESERVOIR: CADMIUM SULFATE 0.13M, AMMONIUM SULFATE 0.8M, SODIUM ACETATE 0.1M PH 5.5, SODIUM AZIDE 0.003M. DROP: 2 UL PROTEIN AND 2 UL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97991 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 14, 2003 / Details: TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING. |
Radiation | Monochromator: FIRST CRYSTAL FLAT AND N2 COOLED. SECOND ONE SAGITALLY BENT. SI(111) OR SI(311) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97991 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 21041 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V2I Resolution: 1.9→105.41 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.388 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.119 / 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: 19.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→105.41 Å
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Refine LS restraints |
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