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- PDB-1jh6: Semi-reduced Cyclic Nucleotide Phosphodiesterase from Arabidopsis... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jh6 | ||||||
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Title | Semi-reduced Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana | ||||||
![]() | cyclic phosphodiesterase | ||||||
![]() | HYDROLASE / ADP-ribose 1'' / 2''-cyclic phosphate / RNA processing / 2' / 3'-cyclic nucleotide phosphodiesterase | ||||||
Function / homology | ![]() cyclic nucleotide metabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / tRNA splicing, via endonucleolytic cleavage and ligation / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hofmann, A. / Grella, M. / Botos, I. / Filipowicz, W. / Wlodawer, A. | ||||||
![]() | ![]() Title: Crystal structures of the semireduced and inhibitor-bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana. Authors: Hofmann, A. / Grella, M. / Botos, I. / Filipowicz, W. / Wlodawer, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.6 KB | Display | ![]() |
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PDB format | ![]() | 69.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
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Full document | ![]() | 455.8 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 21510.268 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O04147, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.9 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5 Details: (NH4)2SO4, NaOAc, DTT, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→32 Å / Num. all: 29387 / Num. obs: 29387 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5 % / Rmerge(I) obs: 0.474 / % possible all: 95.7 |
Reflection | *PLUS Lowest resolution: 32 Å / Num. measured all: 306271 |
Reflection shell | *PLUS % possible obs: 95.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: oxidised CPDase (A. thaliana) [delta 90-115] Resolution: 1.8→32.43 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 68699.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.04 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→32.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 32 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.295 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.288 |