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Open data
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Basic information
Entry | Database: PDB / ID: 6mc8 | ||||||
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Title | Crystal structure of PprA dimer from Deinococcus deserti | ||||||
![]() | DNA repair protein PprA | ||||||
![]() | DNA BINDING PROTEIN / DNA damage repair / Radiation induced / Genome segregation / Filament formation | ||||||
Function / homology | Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / aspartic-type endopeptidase activity / Putative DNA repair protein PprA![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Szabla, R. / Junop, M.S. / Rok, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of PprA from Deinococcus radiodurans Authors: Szabla, R. / Czerwinski, M. / Junop, M.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.6 KB | Display | ![]() |
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PDB format | ![]() | 90.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.6 KB | Display | ![]() |
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Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 33631.777 Da / Num. of mol.: 2 / Mutation: D192K, D196K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: VCD115 / DSM 17065 / LMG 22923 / Gene: pprA, Deide_2p01380 / Plasmid: pDEST-527 Details (production host): Gateway destination vector for bacterial expression; His tag Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.51 % / Description: square bipyramid |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: Protein at 3.0 mg/mL in 800 mM NaCl, 150 mM Imidazole, 20 mM Tris, pH 8.0 was mixed in 1:1 volume ratio with MCSG3 #92 - a solution of 30 % (w/v) PEG 400 and 0.1 M CHES, pH 9.5. The drop was ...Details: Protein at 3.0 mg/mL in 800 mM NaCl, 150 mM Imidazole, 20 mM Tris, pH 8.0 was mixed in 1:1 volume ratio with MCSG3 #92 - a solution of 30 % (w/v) PEG 400 and 0.1 M CHES, pH 9.5. The drop was suspended over 1.5M Ammonium sulfate. Temp details: Constant-temperature incubation |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Nitrogen gas cryostream |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→28.72 Å / Num. obs: 22737 / % possible obs: 96.7 % / Redundancy: 24.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.049 / Rrim(I) all: 0.189 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2 / Num. unique obs: 2079 / CC1/2: 0.845 / Rpim(I) all: 0.223 / Rrim(I) all: 0.7 / % possible all: 80.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.5→28.72 Å
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