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Yorodumi- PDB-2ydb: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ydb | ||||||
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Title | Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, soaked with 2',3'-cyclic NADP | ||||||
Components | 2', 3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE | ||||||
Keywords | HYDROLASE / MYELIN / NERVOUS SYSTEM | ||||||
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: 2.15 Å | ||||||
Authors | Myllykoski, M. / Kursula, P. | ||||||
Citation | Journal: Plos One / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ydb.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ydb.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ydb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/2ydb ftp://data.pdbj.org/pub/pdb/validation_reports/yd/2ydb | HTTPS FTP |
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-Related structure data
Related structure data | 2xmiSC 2y1pC 2y3xC 2yddC 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, RESIDUES 159-378 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PTH 27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase |
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#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | NICOTINAMI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | pH: 3.5 Details: CRYSTALLIZATION: 50 MM NA-CITRATE PH 3.5 & 30 % PEG 3000, SOAKING: 50 MM NA-CITRATE PH 3.5, 35 % PEG 1500 & 100 MM 2,3-CYCLIC NADP FOR 25 MIN |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796 |
Detector | Type: MARRESEARCH MAR165 / Detector: CCD / Date: May 14, 2010 Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M) |
Radiation | Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03796 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→25 Å / Num. obs: 11501 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 35.61 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.17 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XMI Resolution: 2.15→23.452 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 26.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.098 Å2 / ksol: 0.396 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→23.452 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -3.9799 Å / Origin y: 7.0768 Å / Origin z: -15.3398 Å
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Refinement TLS group | Selection details: ALL |