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Yorodumi- PDB-5zda: Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zda | ||||||
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Title | Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in apo form | ||||||
Components | poly ADP-ribose glycohydrolase | ||||||
Keywords | 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 / Microbial-type PARG catalytic domain-containing protein Function and homology information | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.548 Å | ||||||
Authors | Cho, C.C. / Hsu, C.H. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nat Commun / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zda.cif.gz | 116.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zda.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 5zda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zda_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 5zda_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 5zda_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5zda_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/5zda ftp://data.pdbj.org/pub/pdb/validation_reports/zd/5zda | HTTPS FTP |
-Related structure data
Related structure data | 5zdbC 5zdcC 5zddC 5zdeC 5zdfC 5zdgC 3sihS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27754.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: DR_B0099 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RZM4 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.04 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M Li2SO4, 0.1 M Bis-Tris pH 6.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.548→26.21 Å / Num. obs: 33721 / % possible obs: 97.66 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.53 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.391 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SIH Resolution: 1.548→26.209 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.548→26.209 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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