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- PDB-6tb5: The crystal structure of the DPS2 from DEINOCOCCUS RADIODURANS to... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tb5 | ||||||
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Title | The crystal structure of the DPS2 from DEINOCOCCUS RADIODURANS to 1.83A resolution (sequentially soaked in CaCl2 [5mM] for 20 min, then in Ammonium iron(II) sulfate [10mM] for 2h). | ||||||
![]() | DNA protection during starvation protein 2 | ||||||
![]() | DNA BINDING PROTEIN / Iron biomineralisation / iron storage / iron detoxification / DNA binding / Calcium binding. | ||||||
Function / homology | ![]() Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cuypers, M.G. / McSweeney, S. / Romao, C.V. / Mitchell, E.P. | ||||||
![]() | ![]() Title: The crystal structure of the DPS2 from DEINOCOCCUS RADIODURANS to 1.83A resolution (sequentially soaked in CaCl2 [5mM] for 20 min, then in Ammonium iron(II) sulfate [10mM] for 2h). Authors: Cuypers, M.G. / McSweeney, S. / Romao, C.V. / Mitchell, E.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.3 KB | Display | ![]() |
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PDB format | ![]() | 37 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c6rS S: Starting model for refinement |
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Similar structure data |
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Links
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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
#1: Protein | Mass: 23289.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dps2, dps-2, DR_B0092 / Plasmid: PDEST14 / Production host: ![]() ![]() References: UniProt: Q9RZN1, Oxidoreductases; Oxidizing metal ions | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FE / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.1 % / Description: cubes |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M KCl, 0.01M MgCl2, 0.05M HEPES pH 7.0, 5% v/v PEG400 (NATRIX #35) Temp details: controlled temperature room |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: cryostream frozeon on beamline goniometer Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→29.61 Å / Num. obs: 20877 / % possible obs: 99.8 % / Redundancy: 19.6 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.028 / Rrim(I) all: 0.123 / Χ2: 0.98 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.83→1.87 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 2 / Num. unique obs: 1294 / CC1/2: 0.726 / Rpim(I) all: 0.41 / Χ2: 0.84 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2C6R Resolution: 1.83→28.09 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.61 Å2 / Biso mean: 39.0355 Å2 / Biso min: 17.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→28.09 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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