[English] 日本語
Yorodumi- PDB-3zwp: Crystal structure of ADP ribosyl cyclase complexed with ara-2'F-A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zwp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ADP ribosyl cyclase complexed with ara-2'F-ADP- ribose at 2.1 angstrom | ||||||
Components | ADP-RIBOSYL CYCLASECyclic ADP-ribose | ||||||
Keywords | HYDROLASE / DP-RIBOSYL CYCLASE / CD38 / APLYSIA / BINDING SITES / HYDROLYSIS / NAD / PROTEIN CONFORMATION / SUBSTRATE SPECIFICITY | ||||||
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: 2.11 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zwp.cif.gz | 865.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zwp.ent.gz | 721.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/3zwp ftp://data.pdbj.org/pub/pdb/validation_reports/zw/3zwp | HTTPS FTP |
---|
-Related structure data
Related structure data | 3zwmC 3zwnC 3zwoC 3zwvC 3zwwC 1r12S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||
4 |
| ||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-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-AVU / [( #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE ADDITIONAL ALANINE RESIDUES AT THE N-TERMINUS ARE ACTUALLY LEFT OVER FROM THE CLEAVAGE OF THE ...THE ADDITIONAL | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.62 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 / Details: 0.1 M IMIDAZOLE, PH 7.5, 12-14% PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 141088 / % possible obs: 95.1 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / % possible all: 80.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R12 Resolution: 2.11→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.248 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 44.882 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|