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- PDB-5zde: Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zde | ||||||
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Title | Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P3221) | ||||||
![]() | Poly ADP-ribose glycohydrolase | ||||||
![]() | HYDROLASE / ADP-ribose / poly(ADP-ribose) glycohydrolase | ||||||
Function / homology | ![]() Conserved hypothetical protein CHP02452 / Microbial-type PARG, catalytic domain / Microbial-type PARG, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cho, C.C. / Hsu, C.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and biochemical evidence supporting poly ADP-ribosylation in the bacterium Deinococcus radiodurans. Authors: Cho, C.C. / Chien, C.Y. / Chiu, Y.C. / Lin, M.H. / Hsu, C.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127 KB | Display | ![]() |
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PDB format | ![]() | 86.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478 KB | Display | ![]() |
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Full document | ![]() | 481.5 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zdaC ![]() 5zdbC ![]() 5zdcC ![]() 5zddC ![]() 5zdfC ![]() 5zdgC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27389.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: DR_B0099 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-AR6 / [( |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.53 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20 % 2-Propanol, 20% Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.803→27.234 Å / Num. obs: 7430 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 44.69 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 30.11 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→27.23 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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