+Open data
-Basic information
Entry | Database: PDB / ID: 5m31 | ||||||
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Title | Macrodomain of Thermus aquaticus DarG | ||||||
Components | Appr-1-p processing domain protein | ||||||
Keywords | ANTITOXIN / macrodomain / ADP-ribosylation / ADP-ribose / toxin-antitoxin | ||||||
Function / homology | Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Appr-1-p processing domain protein Function and homology information | ||||||
Biological species | Thermus aquaticus Y51MC23 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Ariza, A. | ||||||
Citation | Journal: Mol. Cell / Year: 2016 Title: The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA. Authors: Jankevicius, G. / Ariza, A. / Ahel, M. / Ahel, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m31.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m31.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 5m31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/5m31 ftp://data.pdbj.org/pub/pdb/validation_reports/m3/5m31 | HTTPS FTP |
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-Related structure data
Related structure data | 5m3eSC 5m3iC 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: 18784.666 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: codon optimised gene / Source: (gene. exp.) Thermus aquaticus Y51MC23 (bacteria) / Gene: TaqDRAFT_4250 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: B7A854 | ||||
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#2: Chemical | #3: Chemical | #4: 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: 2.31 Å3/Da / Density % sol: 46.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 8% (w/v) PEG 20000, 8% (w/v) PEG 500 MME, 200 mM potassium thiocyanate, 100 mM sodium acetate (pH5.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98999 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98999 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→41.16 Å / Num. obs: 18354 / % possible obs: 96.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.67→1.71 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2 / CC1/2: 0.771 / % possible all: 79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M3E Resolution: 1.67→41.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.389 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.849 Å2
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Refinement step | Cycle: 1 / Resolution: 1.67→41.16 Å
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Refine LS restraints |
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