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Yorodumi- PDB-4a25: X-ray structure Dps from Kineococcus radiotolerans in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a25 | ||||||
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Title | X-ray structure Dps from Kineococcus radiotolerans in complex with Mn (II) ions. | ||||||
Components | FERRITIN DPS FAMILY PROTEIN | ||||||
Keywords | METAL BINDING PROTEIN / DETOXIFICATION PROCESS | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis Similarity search - Function | ||||||
Biological species | KINEOCOCCUS RADIOTOLERANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ilari, A. / Fiorillo, A. / Ardini, M. / Stefanini, S. / Chiancone, E. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Kineococcus Radiotolerans Dps Forms a Heteronuclear Mn-Fe Ferroxidase Center that May Explain the Mn-Dependent Protection Against Oxidative Stress. Authors: Ardini, M. / Fiorillo, A. / Fittipaldi, M. / Stefanini, S. / Gatteschi, D. / Llari, A. / Chiancone, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a25.cif.gz | 274.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a25.ent.gz | 224.6 KB | Display | PDB format |
PDBx/mmJSON format | 4a25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/4a25 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/4a25 | HTTPS FTP |
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-Related structure data
Related structure data | 2z90S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 18519.654 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KINEOCOCCUS RADIOTOLERANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6WG04 #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.36 % / Description: NONE |
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Crystal grow | pH: 8 Details: MPD (2-METHYL-2,4-PENTANEDIOL) 45 %, TRIS-HCL 0.1 M, PH 8.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 49300 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 16.7 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 40.94 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 7.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z90 Resolution: 2→75.24 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.849 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.162 / 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: 31.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2→75.24 Å
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Refine LS restraints |
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