+Open data
-Basic information
Entry | Database: PDB / ID: 4am5 | ||||||
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Title | Bacterioferritin from Blastochloris viridis | ||||||
Components | BACTERIOFERRITIN | ||||||
Keywords | METAL BINDING PROTEIN / FERROXIDASE CENTRE / IRON STORAGE / DI IRON CENTRE / IRON CHANNEL / HEME BINDING | ||||||
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: 1.58 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4am5.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4am5.ent.gz | 66.2 KB | Display | PDB format |
PDBx/mmJSON format | 4am5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4am5_validation.pdf.gz | 801.5 KB | Display | wwPDB validaton report |
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Full document | 4am5_full_validation.pdf.gz | 805.6 KB | Display | |
Data in XML | 4am5_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 4am5_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4am5 ftp://data.pdbj.org/pub/pdb/validation_reports/am/4am5 | HTTPS FTP |
-Related structure data
Related structure data | 4am2C 4am4C 3gvyS 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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Unit cell |
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Components on special symmetry positions |
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-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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.13 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1 UL PROTEIN PLUS 1 UL RESERVOIR SOLUTION OF 0.1 M HEPES PH 7.5, 0.1 M NACL, 1.6 M (NH4)2SO4 USING THE HANGING-DROP VAPOR-DIFFUSION METHOD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97625 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→39.1 Å / Num. obs: 52949 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 41 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.84 |
Reflection shell | Resolution: 1.58→1.62 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.25 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GVY Resolution: 1.58→98.27 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.074 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.067 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.655 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→98.27 Å
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