+Open data
-Basic information
Entry | Database: PDB / ID: 5ae0 | |||||||||
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Title | Perdeuterated mouse CNPase catalytic domain at atomic resolution | |||||||||
Components | 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath abaxonal region / myelin sheath adaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus ...cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath abaxonal region / myelin sheath adaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus / forebrain development / axonogenesis / adult locomotory behavior / cell projection / response to toxic substance / melanosome / myelin sheath / mitochondrial inner membrane / microtubule / mitochondrial outer membrane / response to lipopolysaccharide / perinuclear region of cytoplasm / extracellular space / RNA binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | |||||||||
Authors | Laulumaa, S. / Kursula, P. | |||||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase. Authors: Raasakka, A. / Myllykoski, M. / Laulumaa, S. / Lehtimaki, M. / Hartlein, M. / Moulin, M. / Kursula, I. / Kursula, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ae0.cif.gz | 174.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ae0.ent.gz | 143.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ae0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5ae0 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5ae0 | HTTPS FTP |
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-Related structure data
Related structure data | 4wbiC 4wblC 4wc9C 4wcaC 4wcbC 4wccC 4wdaC 4wdbC 4wddC 4wdeC 4wdfC 4wdgC 4wdhC 4wexC 4wfrC 2wutS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 24293.928 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 179-398 Source method: isolated from a genetically manipulated source Details: PERDEUTERATED / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETNKI-HIS3C-LIC-KAN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-CL / |
#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: 1.97 Å3/Da / Density % sol: 37.59 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 25% PEG3350, 50 MM ACETATE, PD 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.913 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.913 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→30 Å / Num. obs: 90347 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 8.77 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.04→1.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 1.1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WUT Resolution: 1.04→29.287 Å / SU ML: 0.1 / σ(F): 1.99 / Phase error: 17.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→29.287 Å
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Refine LS restraints |
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LS refinement shell |
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