+
Open data
-
Basic information
Entry | Database: PDB / ID: 1r15 | ||||||
---|---|---|---|---|---|---|---|
Title | Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P | ||||||
![]() | ADP-ribosyl cyclase | ||||||
![]() | HYDROLASE / ADP-ribosyl cyclase / cyclic ADP-ribose / NAADP / Ca2+ signalling | ||||||
Function / homology | ![]() 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / single fertilization / positive regulation of B cell proliferation / transferase activity / cytoplasmic vesicle / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Love, M.L. / Szebenyi, D.M.E. / Kriksunov, I.A. / Thiel, D.J. / Munshi, C. / Graeff, R. / Lee, H.C. / Hao, Q. | ||||||
![]() | ![]() Title: ADP-ribosyl cyclase; crystal structures reveal a covalent intermediate. Authors: Love, M.L. / Szebenyi, D.M. / Kriksunov, I.A. / Thiel, D.J. / Munshi, C. / Graeff, R. / Lee, H.C. / Hao, Q. | ||||||
History |
| ||||||
Remark 600 | HETEROGEN THE R5P UNDERGOES REACTION WITH THE PROTEIN TO FORM A 1-DEOXY INTERMEDIATE, LABELLED N, 1- ...HETEROGEN THE R5P UNDERGOES REACTION WITH THE PROTEIN TO FORM A 1-DEOXY INTERMEDIATE, LABELLED N, 1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE. THE N IS COVALENTLY BOUND TO THE PROTEIN. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 394.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 335.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 535.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 620.5 KB | Display | |
Data in XML | ![]() | 82 KB | Display | |
Data in CIF | ![]() | 100.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 29579.945 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Chemical | ChemComp-N / #3: Chemical | ChemComp-NCA / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.63 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 316 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Imidazole and 12-24 % PEG 4K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 316K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / Details: Munshi, C., (1999) J. Biol. Chem., 274, 30770. | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→33 Å / Num. all: 64996 / Num. obs: 57197 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.108 |
Reflection | *PLUS Rmerge(I) obs: 0.108 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / % possible obs: 44.7 % / Rmerge(I) obs: 0.31 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→33 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 57197 / Rfactor Rfree: 0.2694 / Rfactor Rwork: 0.2439 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |