[English] 日本語
Yorodumi- PDB-2v2i: Wild type recombinant horse spleen apoferritin cocrystallized wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v2i | ||||||
---|---|---|---|---|---|---|---|
Title | Wild type recombinant horse spleen apoferritin cocrystallized with haemin in acidic conditions | ||||||
Components | FERRITIN LIGHT CHAIN | ||||||
Keywords | METAL TRANSPORT / IRON / HAEMIN / 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: 2 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 |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2v2i.cif.gz | 56 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2v2i.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 2v2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v2i_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2v2i_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 2v2i_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 2v2i_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/2v2i ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v2i | HTTPS FTP |
-Related structure data
Related structure data | 2v2jC 2v2lC 2v2mC 2v2nC 2v2oC 2v2pC 2v2rC 2v2sC 2w0oC 1hrsS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24|||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 19987.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) EQUUS CABALLUS (horse) / Organ: SPLEEN / Plasmid: PMK2100 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): BMH-71-18 / References: UniProt: P02791 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
---|---|
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 2UL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2→20 Å / Num. obs: 18049 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.2 / % possible all: 96.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HRS Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.926 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.91 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|