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- PDB-2o3q: Structural Basis for Formation and Hydrolysis of Calcium Messenge... -
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Basic information
Entry | Database: PDB / ID: 2o3q | ||||||
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Title | Structural Basis for Formation and Hydrolysis of Calcium Messenger Cyclic ADP-ribose by Human CD38 | ||||||
![]() | ADP-ribosyl cyclase 1 | ||||||
![]() | HYDROLASE / Human CD38 E226Q mutant / the catalytic pocket / cADPR formation and hydrolysis / substrate binding | ||||||
Function / homology | ![]() 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of bone resorption / long-term synaptic depression ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of bone resorption / long-term synaptic depression / response to hydroperoxide / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / response to progesterone / female pregnancy / apoptotic signaling pathway / B cell receptor signaling pathway / positive regulation of insulin secretion / negative regulation of neuron projection development / response to estradiol / positive regulation of cytosolic calcium ion concentration / transferase activity / positive regulation of cell growth / basolateral plasma membrane / nuclear membrane / response to hypoxia / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Q. / Kriksunov, I.A. / Graeff, R. / Lee, H.C. / Hao, Q. | ||||||
![]() | ![]() Title: Structural basis for formation and hydrolysis of the calcium messenger cyclic ADP-ribose by human CD38 Authors: Liu, Q. / Kriksunov, I.A. / Graeff, R. / Lee, H.C. / Hao, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 123.7 KB | Display | ![]() |
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PDB format | ![]() | 93.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2o3rC ![]() 2o3sC ![]() 2o3tC ![]() 2o3uC ![]() 1yh3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | There are two biological units in the crystallographic asymmetric unit. |
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Components
#1: Protein | Mass: 30379.408 Da / Num. of mol.: 2 / Fragment: Extracellular domain, residues 45-300 / Mutation: Q49T, N100D, N164D, N209D, N219D, E226Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.93 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, 12% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2006 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→30 Å / Num. all: 37397 / Num. obs: 34368 / % possible obs: 91.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 1.98→2.05 Å / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1YH3 Resolution: 1.98→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.438 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.23 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 34.171 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.034 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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