+Open data
-Basic information
Entry | Database: PDB / ID: 5h46 | ||||||
---|---|---|---|---|---|---|---|
Title | Mycobacterium smegmatis Dps1 mutant - F47E | ||||||
Components | DNA protection during starvation protein | ||||||
Keywords | OXIDOREDUCTASE / Structural switch / Mutational tipping point / Point mutant / Oligomerisation | ||||||
Function / homology | Function and homology information Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / ferric iron binding / intracellular iron ion homeostasis / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Williams, S.M. / Chandran, A.V. / Vijayan, M. / Chatterji, D. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Structure / Year: 2017 Title: A Mutation Directs the Structural Switch of DNA Binding Proteins under Starvation to a Ferritin-like Protein Cage. Authors: Williams, S.M. / Chandran, A.V. / Prakash, S. / Vijayan, M. / Chatterji, D. #1: Journal: Biochemistry / Year: 2008 Title: Molecular mechanism of in vitro oligomerization of Dps from Mycobacterium smegmatis: mutations of the residues identified by "interface cluster" analysis. Authors: Chowdhury, R.P. / Vijayabaskar, M.S. / Vishveshwara, S. / Chatterji, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5h46.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5h46.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 5h46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h46_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5h46_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 5h46_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 5h46_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/5h46 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/5h46 | HTTPS FTP |
-Related structure data
Related structure data | 1veiS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16815.914 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 9-157 / Mutation: F47E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: dps, MSMEG_6467, MSMEI_6295 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) References: UniProt: A0R692, Oxidoreductases; Oxidizing metal ions | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.55 % |
---|---|
Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 / Details: 100 mM Na-HEPES, 200 mM CaCl2, 10% PEG 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 5, 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: 2.85→39.147 Å / Num. obs: 5200 / % possible obs: 99.9 % / Redundancy: 42.7 % / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 3→3.16 Å / CC1/2: 0.68 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VEI Resolution: 2.85→39.147 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 38.363 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R: 1.085 / ESU R Free: 0.367 / 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: 103.235 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.85→39.147 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|