+
Open data
-
Basic information
Entry | Database: PDB / ID: 6tmm | ||||||
---|---|---|---|---|---|---|---|
Title | BIL2 domain from T.thermophila BUBL1 locus (C1A-N143A) | ||||||
![]() | (NAD(P)(+)--arginine ADP- ...) x 2 | ||||||
![]() | SPLICING / Intein / PTM / ubiquitin | ||||||
Function / homology | ![]() NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / intein-mediated protein splicing / nucleotidyltransferase activity / modification-dependent protein catabolic process / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chiarini, V. / Ilari, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 140.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 483.8 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
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.) ![]() Gene: TTHERM_00085190 / Production host: ![]() ![]() 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.) ![]() Gene: TTHERM_00085190 / Production host: ![]() ![]() References: UniProt: Q236S9, NAD+-protein-arginine ADP-ribosyltransferase |
---|
-Non-polymers , 5 types, 140 molecules ![](data/chem/img/FMT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-HG / #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.63 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.398→69.602 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|