+Open data
-Basic information
Entry | Database: PDB / ID: 4am2 | ||||||
---|---|---|---|---|---|---|---|
Title | Bacterioferritin from Blastochloris viridis | ||||||
Components | BACTERIOFERRITIN | ||||||
Keywords | METAL BINDING PROTEIN / FERROXIDASE CENTRE / IRON STORAGE / DI IRON CENTRE / IRON CHANNEL | ||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / heme binding / cytosol Similarity search - Function | ||||||
Biological species | BLASTOCHLORIS VIRIDIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wahlgren, W.Y. / Omran, H. / von Stetten, D. / Royant, A. / van der Post, S. / Katona, G. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structural Characterization of Bacterioferritin from Blastochloris Viridis. Authors: Wahlgren, W.Y. / Omran, H. / von Stetten, D. / Royant, A. / van der Post, S. / Katona, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4am2.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4am2.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 4am2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4am2 ftp://data.pdbj.org/pub/pdb/validation_reports/am/4am2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4am4C 4am5C 3gvyS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 12||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18390.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: K7N5M0*PLUS #2: Chemical | ChemComp-HEM / | #3: Chemical | ChemComp-FE / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1UL PROTEIN PLUS 1UL RESERVOIR SOLUTION OF 0.1M HEPES PH7.5, 0.1M NACL, 1.6M (NH4)2SO4 USING THE HANGING- DROP VAPOR-DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.87 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.7 Å / Num. obs: 35784 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.5 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GVY Resolution: 1.8→98.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.048 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.106 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.608 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→98.26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|