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Yorodumi- PDB-2pgl: Catalysis associated conformational changes revealed by human CD3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pgl | ||||||
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Title | Catalysis associated conformational changes revealed by human CD38 complexed with a non-hydrolyzable substrate analog | ||||||
Components | ADP-ribosyl cyclase 1Cyclic ADP-ribose | ||||||
Keywords | HYDROLASE / Human CD38 E226Q mutant bound with N1-cIDPR / the catalytic pocket / conformational changes of the active site / substrate analog binding | ||||||
Function / homology | Function and homology information 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NADP+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of bone resorption ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NADP+ nucleosidase activity / 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 / response to estradiol / negative regulation of neuron projection development / 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: 1.76 Å | ||||||
Authors | Liu, Q. / Kriksunov, I.A. / Moreau, C. / Graeff, R. / Potter, B.V.L. / Lee, H.C. / Hao, Q. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Catalysis-associated Conformational Changes Revealed by Human CD38 Complexed with a Non-hydrolyzable Substrate Analog Authors: Liu, Q. / Kriksunov, I.A. / Moreau, C. / Graeff, R. / Potter, B.V. / 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 | 2pgl.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pgl.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/2pgl ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pgl | HTTPS FTP |
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-Related structure data
Related structure data | 2pgjC 2o3tS 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: 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.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P28907, NAD+ glycohydrolase #2: Chemical | ChemComp-N1C / | #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: 2.3 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES, pH 6.0, and 15% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-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: May 1, 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: 1.75→30 Å / Num. all: 53485 / Num. obs: 51667 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 1.87 / Num. unique all: 4854 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2O3T Resolution: 1.76→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.318 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.146 / ESU R Free: 0.135 / 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: 36.248 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.804 Å / Total num. of bins used: 20
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