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Yorodumi- PDB-2i67: Structural Basis for the Mechanistic Understanding Human CD38 Con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i67 | ||||||
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Title | Structural Basis for the Mechanistic Understanding Human CD38 Controlled Multiple Catalysis | ||||||
Components | ADP-ribosyl cyclase 1Cyclic ADP-ribose | ||||||
Keywords | HYDROLASE / the catalytic pocket / reaction product / reaction intermediate | ||||||
Function / homology | Function and homology information phosphorus-oxygen lyase activity / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / artery smooth muscle contraction / Nicotinate metabolism / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / response to hydroperoxide ...phosphorus-oxygen lyase activity / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / artery smooth muscle contraction / Nicotinate metabolism / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / response to hydroperoxide / negative regulation of bone resorption / 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 / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Liu, Q. / Kriksunov, I.A. / Graeff, R. / Munshi, C. / Lee, H.C. / Hao, Q. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural basis for the mechanistic understanding of human CD38-controlled multiple catalysis. Authors: Liu, Q. / Kriksunov, I.A. / Graeff, R. / Munshi, C. / Lee, H.C. / Hao, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i67.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i67.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 2i67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/2i67 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/2i67 | HTTPS FTP |
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-Related structure data
Related structure data | 2i65C 2i66C 1yh3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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. |
-Components
#1: Protein | Mass: 30380.393 Da / Num. of mol.: 2 / Mutation: Q49T, N100D, N164D, N209D, N219D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P28907, NAD+ glycohydrolase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, 12% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 17, 2005 |
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: 1.7→50 Å / Num. all: 54974 / Num. obs: 52170 / % possible obs: 94.9 % / Observed criterion σ(F): 3.3 / Observed criterion σ(I): 3.3 |
Reflection shell | Resolution: 1.7→1.76 Å / % possible all: 71.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YH3 Resolution: 1.71→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.809 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.127 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.576 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.707→1.751 Å / Total num. of bins used: 20
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