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Yorodumi- PDB-1jh7: Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jh7 | ||||||
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Title | Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana | ||||||
Components | cyclic phosphodiesterase | ||||||
Keywords | HYDROLASE / ADP-ribose 1'' / 2''-cyclic phosphate / RNA processing / 2' / 3'-cyclic nucleotide phosphodiesterase / 3'-cyclic uridine vanadate | ||||||
Function / homology | Function and homology information 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 | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Hofmann, A. / Grella, M. / Botos, I. / Filipowicz, W. / Wlodawer, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jh7.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jh7.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jh7_validation.pdf.gz | 946.4 KB | Display | wwPDB validaton report |
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Full document | 1jh7_full_validation.pdf.gz | 963.8 KB | Display | |
Data in XML | 1jh7_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 1jh7_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/1jh7 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/1jh7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET11d+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O04147, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.1 Å3/Da / Density % sol: 41.7 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5 Details: (NH4)2SO4, NaOAc, DTT, 2',3'-cyclic uridine vanadate, 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: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.07 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 7212 / Num. obs: 7212 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.466 / % possible all: 95.4 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 5960 / Num. measured all: 87738 |
Reflection shell | *PLUS % possible obs: 95.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: semi-reduced CPDase (A. thaliana) [delta 90-115] Resolution: 2.4→25.29 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 185038.81 / 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: 236.9 Å2 / ksol: 0.357 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→25.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.048 / 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: 50 Å / σ(F): 0 / % reflection Rfree: 10.9 % / Rfactor obs: 0.213 / Rfactor Rfree: 0.398 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 59.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.477 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.431 |