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- PDB-5zdb: 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: 5zdb | ||||||
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Title | Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P21) | ||||||
![]() | 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 | ![]() | 214.5 KB | Display | ![]() |
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PDB format | ![]() | 169.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zdaSC ![]() 5zdcC ![]() 5zddC ![]() 5zdeC ![]() 5zdfC ![]() 5zdgC S: Starting model for refinement 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27600.174 Da / Num. of mol.: 2 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: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M Sodium citrate tribasic dihydrate pH 6.0, 10% 2-Propanol, 10% 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: May 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.972→25.959 Å / Num. obs: 33944 / % possible obs: 98.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.353 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.019 / % possible all: 91.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZDA Resolution: 1.972→25.959 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.972→25.959 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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