+Open data
-Basic information
Entry | Database: PDB / ID: 7qzs | ||||||
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Title | Crystal structure of mouse CNPase catalytic domain, G324D mutant | ||||||
Components | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | ||||||
Keywords | HYDROLASE / CNPase / 2H phosphodiesterase / mutation | ||||||
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: 1.8 Å | ||||||
Authors | Markusson, S. / Kursula, P. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of mouse CNPase catalytic domain, G324D mutant Authors: Markusson, S. / Kursula, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qzs.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qzs.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 7qzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/7qzs ftp://data.pdbj.org/pub/pdb/validation_reports/qz/7qzs | HTTPS FTP |
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-Related structure data
Related structure data | 2xmiS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4641921 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24351.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnp, Cnp1 / Production host: Escherichia coli (E. coli) References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30% (v/v) Jeffamine ED-2003 and 0.1M HEPES (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 17959 / % possible obs: 98.1 % / Redundancy: 7.8 % / Biso Wilson estimate: 30.56 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.15 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1300 / CC1/2: 0.319 / Rrim(I) all: 2.927 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XMI Resolution: 1.8→37.74 Å / SU ML: 0.2678 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4016 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→37.74 Å
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Refine LS restraints |
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LS refinement shell |
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