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- PDB-3i9k: Crystal structure of ADP ribosyl cyclase complexed with substrate NAD -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i9k | ||||||
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Title | Crystal structure of ADP ribosyl cyclase complexed with substrate NAD | ||||||
![]() | ADP-ribosyl cyclase | ||||||
![]() | HYDROLASE / Homodimer / protein substrate NAD complex / ADP-ribosyl cyclase / Disulfide bond / Fertilization / NAD | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Liu, Q. / Graeff, R. / Kriksunov, I.A. / Jiang, H. / Zhang, B. / Oppenheimer, N. / Lin, H. / Potter, B.V.L. / Lee, H.C. / Hao, Q. | ||||||
![]() | ![]() Title: Structural basis for enzymatic evolution from a dedicated ADP-ribosyl cyclase to a multifunctional NAD hydrolase Authors: Liu, Q. / Graeff, R. / Kriksunov, I.A. / Jiang, H. / Zhang, B. / Oppenheimer, N. / Lin, H. / Potter, B.V.L. / Lee, H.C. / Hao, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.2 KB | Display | ![]() |
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PDB format | ![]() | 94.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 833.6 KB | Display | ![]() |
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Full document | ![]() | 840.7 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 38.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i9jC ![]() 3i9lC ![]() 3i9mC ![]() 3i9nC ![]() 1lbeS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29507.883 Da / Num. of mol.: 2 / Mutation: E179G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PPICZ(ALPHA)A / Production host: ![]() #2: Chemical | ChemComp-NAD / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M imidazole, pH 7.5, 12-24% PEG 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 1, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9771 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→30 Å / Num. all: 49177 / Num. obs: 47800 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.83→1.9 Å / % possible all: 84.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LBE Resolution: 1.83→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.056 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.3 Å2 / Biso mean: 31.135 Å2 / Biso min: 16.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.834→1.881 Å / Total num. of bins used: 20
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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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