+Open data
-Basic information
Entry | Database: PDB / ID: 6tmm | ||||||
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Title | BIL2 domain from T.thermophila BUBL1 locus (C1A-N143A) | ||||||
Components | (NAD(P)(+)--arginine ADP- ...) x 2 | ||||||
Keywords | SPLICING / Intein / PTM / ubiquitin | ||||||
Function / homology | Function and homology information NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / intein-mediated protein splicing / nucleotidyltransferase activity Similarity search - Function | ||||||
Biological species | Tetrahymena thermophila SB210 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.398 Å | ||||||
Authors | Chiarini, V. / Ilari, A. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2021 Title: Structural basis of ubiquitination mediated by protein splicing in early Eukarya. Authors: Chiarini, V. / Fiorillo, A. / Camerini, S. / Crescenzi, M. / Nakamura, S. / Battista, T. / Guidoni, L. / Colotti, G. / Ilari, A. #1: Journal: Biochim.Biophys.Acta / Year: 2021 Title: Structural basis of ubiquitination mediated by protein splicing in early Eukarya Authors: Chiarini, V. / Fiorillo, A. / Camerini, S. / Crescenzi, M. / Nakamura, S. / Battista, T. / Guidoni, L. / Colotti, G. / Ilari, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tmm.cif.gz | 140.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tmm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/6tmm ftp://data.pdbj.org/pub/pdb/validation_reports/tm/6tmm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB CCC DDD) |
-Components
-NAD(P)(+)--arginine ADP- ... , 2 types, 4 molecules AAACCCBBBDDD
#1: Protein | Mass: 17842.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote) Gene: TTHERM_00085190 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q236S9, NAD+-protein-arginine ADP-ribosyltransferase #2: Protein | Mass: 17729.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote) Gene: TTHERM_00085190 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q236S9, NAD+-protein-arginine ADP-ribosyltransferase |
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-Non-polymers , 5 types, 140 molecules
#3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-HG / #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: Mg formate 0.1 M, PEG3350 19%, Tris 50 mM, NaCl 250 mM. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.398→69.602 Å / Num. obs: 26317 / % possible obs: 98.9 % / Redundancy: 3.36 % / Biso Wilson estimate: 58.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.071 / Net I/σ(I): 12.25 |
Reflection shell | Resolution: 2.398→2.54 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 8236 / CC1/2: 0.733 / Rrim(I) all: 0.704 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.398→69.602 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.873 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.298 Details: Hydrogens have been added in their 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: 56.817 Å2
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Refinement step | Cycle: LAST / Resolution: 2.398→69.602 Å
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Refine LS restraints |
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LS refinement shell |
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