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Yorodumi- PDB-5ww5: Crystal structure of the second DNA-Binding protein under starvat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ww5 | ||||||
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Title | Crystal structure of the second DNA-Binding protein under starvation from Mycobacterium smegmatis soaked with iron in the ratio of 100 iron atoms per dodecamer | ||||||
Components | Putative starvation-induced DNA protecting protein/Ferritin and Dps | ||||||
Keywords | DNA BINDING PROTEIN / ferritin-like fold / DNA binding / ferroxidation / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.04 Å | ||||||
Authors | Williams, S.M. / Chatterji, D. | ||||||
Citation | Journal: Metallomics / Year: 2017 Title: Flexible aspartates propel iron to the ferroxidation sites along pathways stabilized by a conserved arginine in Dps proteins from Mycobacterium smegmatis Authors: Williams, S.M. / Chatterji, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ww5.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ww5.ent.gz | 112.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ww5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/5ww5 ftp://data.pdbj.org/pub/pdb/validation_reports/ww/5ww5 | HTTPS FTP |
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-Related structure data
Related structure data | 5ww3C 5ww4C 5ww6C 5ww7C 5ww8C 5ww9C 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 17854.863 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: MC2 155 / Gene: MSMEG_3242, MSMEI_3159 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QXB7 |
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-Non-polymers , 5 types, 457 molecules
#2: Chemical | #3: Chemical | ChemComp-FE2 / #4: Chemical | #5: Chemical | #6: 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: 2.34 Å3/Da / Density % sol: 47.41 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 6 Details: 100 mM sodium cacodylate, 150 mM MgCl2, 20% PEG3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30 Å / Num. obs: 41644 / % possible obs: 96 % / Redundancy: 8.6 % / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 8.4 / % possible all: 79.8 |
-Processing
Software |
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Refinement | Resolution: 2.04→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.43 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.038 Å2
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Refinement step | Cycle: 1 / Resolution: 2.04→30 Å
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Refine LS restraints |
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