+Open data
-Basic information
Entry | Database: PDB / ID: 4ogw | ||||||
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Title | Structure of a human CD38 mutant complexed with NMN | ||||||
Components | ADP-ribosyl cyclase 1Cyclic ADP-ribose | ||||||
Keywords | HYDROLASE / ADP-ribosyl cyclase | ||||||
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 / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / 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 / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Shewchuk, L.M. / Preugschat, F. / Carter, L.H. / Boros, E.E. / Moyer, M.B. / Stewart, E.L. / Porter, D.J.T. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2014 Title: A pre-steady state and steady state kinetic analysis of the N-ribosyl hydrolase activity of hCD157. Authors: Preugschat, F. / Carter, L.H. / Boros, E.E. / Porter, D.J. / Stewart, E.L. / Shewchuk, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ogw.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ogw.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ogw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/4ogw ftp://data.pdbj.org/pub/pdb/validation_reports/og/4ogw | HTTPS FTP |
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-Related structure data
Related structure data | 1yh3S 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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Unit cell |
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-Components
#1: Protein | Mass: 29662.609 Da / Num. of mol.: 1 / Fragment: CD38, UNP residues 46-300 / Mutation: N100D, N164D, N209D, N219D, E226Q Source method: isolated from a genetically manipulated source Details: Expressed with a FLAG-6xHis-Tev tag. Tag cleaved prior to crystallization Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Production host: Komagataella pastoris (fungus) / References: UniProt: P28907, NAD+ glycohydrolase |
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#2: Chemical | ChemComp-NMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 23% PEG3350, 0.1M Bis-Tris-Propane, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 31, 2009 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→48.45 Å / Num. all: 15181 / Num. obs: 14373 / % possible obs: 99.66 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 38.8 |
Reflection shell | Resolution: 2.054→2.107 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 9.8 / Num. unique all: 990 / % possible all: 96.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YH3 Resolution: 2.05→48.45 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 4.583 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.263 / ESU R Free: 0.215 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.365 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→48.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.054→2.107 Å / Total num. of bins used: 20
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