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- PDB-3dzf: Crystal structure of human CD38 extracellular domain complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dzf | ||||||
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Title | Crystal structure of human CD38 extracellular domain complexed with a covalent intermediate, ara-F-ribose-5'-phosphate | ||||||
![]() | ADP-ribosyl cyclase 1 | ||||||
![]() | HYDROLASE / covalent intermediate / BETA SHEETS / ALPHA BUNDLE / Diabetes mellitus / Glycoprotein / Membrane / NAD / Receptor / Signal-anchor / Transmembrane | ||||||
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 / response to hydroperoxide ...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 / response to hydroperoxide / long-term synaptic depression / 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. / Jiang, H. / Graeff, R. / Lin, H. / Lee, H.C. / Hao, Q. | ||||||
![]() | ![]() Title: Covalent and Noncovalent Intermediates of an NAD Utilizing Enzyme, Human CD38. Authors: Liu, Q. / Kriksunov, I.A. / Jiang, H. / Graeff, R. / Lin, H. / 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 | ![]() | 322.2 KB | Display | ![]() |
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PDB format | ![]() | 262.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 510.8 KB | Display | ![]() |
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Full document | ![]() | 579 KB | Display | |
Data in XML | ![]() | 68.6 KB | Display | |
Data in CIF | ![]() | 93.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dzgC ![]() 3dzhC ![]() 3dziC ![]() 3dzjC ![]() 3dzkC ![]() 1yh3S 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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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30380.393 Da / Num. of mol.: 6 / Fragment: Enzymatic domain: UNP residues 45-300 / Mutation: Q49T, N100D, N164D, N209D, N219D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Sugar | ChemComp-RF5 / #3: Water | ChemComp-HOH / | Nonpolymer details | AUTHORS STATE THAT THE LIGAND RF5 IN THIS ENTRY IS A REACTION INTERMEDIATE, WITH THE (C1') ATOM ...AUTHORS STATE THAT THE LIGAND RF5 IN THIS ENTRY IS A REACTION INTERMEDIA | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.69 % |
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Crystal grow | Temperature: 298 K / pH: 6 Details: 100 mM MES pH 6.0, 15% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-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: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 90177 / % possible obs: 86.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.485 / % possible all: 75 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YH3 Resolution: 2.01→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.472 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.228 / 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: 38.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.06 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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