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Yorodumi- PDB-3zwm: Crystal structure of ADP ribosyl cyclase complexed with substrate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zwm | ||||||
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Title | Crystal structure of ADP ribosyl cyclase complexed with substrate NAD and product cADPR | ||||||
Components | ADP-RIBOSYL CYLCASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / single fertilization / transferase activity / cytoplasmic vesicle / membrane Similarity search - Function | ||||||
Biological species | APLYSIA CALIFORNICA (California sea hare) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kotaka, M. / Graeff, R. / Zhang, L.H. / Lee, H.C. / Hao, Q. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structural Studies of Intermediates Along the Cyclization Pathway of Aplysia Adp-Ribosyl Cyclase. Authors: Kotaka, M. / Graeff, R. / Chen, Z. / Zhang, L.H. / 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 | 3zwm.cif.gz | 828.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zwm.ent.gz | 692.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/3zwm ftp://data.pdbj.org/pub/pdb/validation_reports/zw/3zwm | HTTPS FTP |
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-Related structure data
Related structure data | 3zwnC 3zwoC 3zwpC 3zwvC 3zwwC 1r12S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 29722.102 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare) Plasmid: PPICZALPHAA / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33 / References: UniProt: P29241, NAD+ glycohydrolase #2: Chemical | ChemComp-NAD / #3: Chemical | #4: 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: 2.85 Å3/Da / Density % sol: 56.8 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1M IMIDAZOLE, PH 7.5, 12-14% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 84316 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 67.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.3 / % possible all: 92.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R12 Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 28.607 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.631 / ESU R Free: 0.335 / 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: 64.945 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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