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Yorodumi- PDB-3i9o: Crystal structure of ADP ribosyl cyclase complexed with ribo-2'F-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i9o | ||||||
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Title | Crystal structure of ADP ribosyl cyclase complexed with ribo-2'F-ADP ribose | ||||||
Components | ADP-ribosyl cyclase | ||||||
Keywords | HYDROLASE / Homodimer / enzyme-reaction-intermediate complex / ADP-ribosyl cyclase / Disulfide bond / Fertilization / NAD | ||||||
Function / homology | Function and homology information 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / single fertilization / positive regulation of B cell proliferation / transferase activity / cytoplasmic vesicle / plasma membrane Similarity search - Function | ||||||
Biological species | Aplysia californica (California sea hare) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Graeff, R. / Liu, Q. / Kriksunov, I.A. / Kotaka, M. / Oppenheimer, N. / Hao, Q. / Lee, H.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Mechanism of cyclizing NAD to cyclic ADP-ribose by ADP-ribosyl cyclase and CD38 Authors: Graeff, R. / Liu, Q. / Kriksunov, I.A. / Kotaka, M. / Oppenheimer, N. / Hao, Q. / Lee, H.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i9o.cif.gz | 112 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i9o.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 3i9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i9o_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3i9o_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3i9o_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3i9o_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/3i9o ftp://data.pdbj.org/pub/pdb/validation_reports/i9/3i9o | HTTPS FTP |
-Related structure data
Related structure data | 1lbeS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 3 / Auth seq-ID: 1 - 251 / Label seq-ID: 1 - 251
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-Components
#1: Protein | Mass: 29579.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aplysia californica (California sea hare) Plasmid: PPICZ(ALPHA)A / Production host: Pichia Pastoris (fungus) / Strain (production host): X-33 (INVITROGEN) / References: UniProt: P29241, NAD+ glycohydrolase #2: Chemical | |
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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: 2.83 Å3/Da / Density % sol: 56.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M imidazole, pH 7.5, 12-24% PEG 4000, 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: 0.9789 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 9, 2008 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 12475 / Num. obs: 12475 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3→3.11 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LBE Resolution: 3→47.4 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 1 / SU B: 44.047 / SU ML: 0.353 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; Both LINKs are covalent intermediates results from biochemical reaction.
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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 max: 123.04 Å2 / Biso mean: 45.491 Å2 / Biso min: 39.93 Å2
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Refinement step | Cycle: LAST / Resolution: 3→47.4 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.003→3.08 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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