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- PDB-2y3x: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y3x | ||||||
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Title | Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, complexed with sulfate | ||||||
![]() | 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE | ||||||
![]() | HYDROLASE / MYELIN / NERVOUS SYSTEM | ||||||
Function / homology | ![]() cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath adaxonal region / myelin sheath abaxonal 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 adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus / forebrain development / adult locomotory behavior / axonogenesis / cell projection / response to toxic substance / melanosome / myelin sheath / mitochondrial outer membrane / response to lipopolysaccharide / mitochondrial inner membrane / perinuclear region of cytoplasm / RNA binding / extracellular space / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Myllykoski, M. / Kursula, P. | ||||||
![]() | ![]() Title: Myelin 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase: Active-Site Ligand Binding and Molecular Conformation. Authors: Myllykoski, M. / Raasakka, A. / Han, H. / Kursula, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 265.6 KB | Display | ![]() |
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PDB format | ![]() | 217.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.3 KB | Display | ![]() |
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Full document | ![]() | 494.8 KB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 37.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xmiSC ![]() 2y1pC ![]() 2ydbC ![]() 2yddC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.9998, -0.01424, 0.01338), Vector: |
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Components
#1: Protein | Mass: 24293.928 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN, RESIDUES 159-378 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 3.5 Details: 50MM NA-CITRATE PH 3.5, 2.9M AMMONIUM SULFATE, 10% PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2009 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.1→35 Å / Num. obs: 38236 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.85 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.98 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.83 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XMI Resolution: 2.1→71.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.021 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.987 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→71.4 Å
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Refine LS restraints |
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