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Yorodumi- PDB-1mc0: Regulatory Segment of Mouse 3',5'-Cyclic Nucleotide Phosphodieste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mc0 | ||||||
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Title | Regulatory Segment of Mouse 3',5'-Cyclic Nucleotide Phosphodiesterase 2A, Containing the GAF A and GAF B Domains | ||||||
Components | 3',5'-cyclic nucleotide phosphodiesterase 2A | ||||||
Keywords | HYDROLASE / GAF DOMAIN / 3' / 5'-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE / 5'-GUANOSINE MONOPHOSPHATE | ||||||
Function / homology | Function and homology information hippocampal mossy fiber / cGMP effects / GAF domain binding / : / cellular response to xenobiotic stimulus => GO:0071466 / : / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / G alpha (s) signalling events / cellular response to macrophage colony-stimulating factor stimulus / cardiac septum development ...hippocampal mossy fiber / cGMP effects / GAF domain binding / : / cellular response to xenobiotic stimulus => GO:0071466 / : / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / G alpha (s) signalling events / cellular response to macrophage colony-stimulating factor stimulus / cardiac septum development / regulation of nitric oxide mediated signal transduction / cellular response to cGMP / coronary vasculature development / positive regulation of vascular permeability / heart valve development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of oxidative phosphorylation / negative regulation of vascular permeability / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / regulation of mitochondrion organization / aorta development / ventricular septum development / cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / TPR domain binding / cGMP-mediated signaling / cGMP catabolic process / phosphate ion binding / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP binding / cellular response to cAMP / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cAMP-mediated signaling / synaptic membrane / positive regulation of inflammatory response / cellular response to mechanical stimulus / presynaptic membrane / heart development / cellular response to lipopolysaccharide / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / membrane raft / axon / dendrite / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.86 Å | ||||||
Authors | Martinez, S. / Wu, A. / Glavas, N. / Tang, X. / Turley, S. / Hol, W. / Beavo, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding. Authors: Martinez, S.E. / Wu, A.Y. / Glavas, N.A. / Tang, X.B. / Turley, S. / Hol, W.G. / Beavo, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mc0.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mc0.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mc0_validation.pdf.gz | 722.3 KB | Display | wwPDB validaton report |
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Full document | 1mc0_full_validation.pdf.gz | 735.7 KB | Display | |
Data in XML | 1mc0_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 1mc0_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/1mc0 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/1mc0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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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-Components
#1: Protein | Mass: 41423.910 Da / Num. of mol.: 1 / Fragment: Regulatory domain (residues 207-566) / Mutation: Y230F, F389L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: PDE2A Plasmid details: pRUNH is a derivative of pMW172. Way, M., Pope, B., Gooch, J., Hawkins, M. & Weeds, A. G. (1990) Embo J 9, 4103-9 Plasmid: pRUNH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q922S4, 3',5'-cyclic-GMP phosphodiesterase |
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#2: Chemical | ChemComp-PCG / |
#3: 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: 4.11 Å3/Da / Density % sol: 70.08 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1,4 butanediol, sodium acetate, dithiothreitol, EDTA, Tris, sodium chloride, 3',5' guanosine monophosphate, leupeptin, pepstatin, phenylmethylsulfonyl flouride, pH 5.0, VAPOR DIFFUSION, ...Details: 1,4 butanediol, sodium acetate, dithiothreitol, EDTA, Tris, sodium chloride, 3',5' guanosine monophosphate, leupeptin, pepstatin, phenylmethylsulfonyl flouride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→19.97 Å / Num. all: 15282 / Num. obs: 15282 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.058 |
Reflection shell | Resolution: 2.86→2.97 Å / Num. unique all: 1380 / Rsym value: 0.408 / % possible all: 87.2 |
Reflection | *PLUS Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 87.2 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.86→19.97 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1838569.21 / Data cutoff high rms absF: 1838569.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.1207 Å2 / ksol: 0.291099 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.86→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.86→2.96 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.221 / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.221 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.459 / Rfactor Rwork: 0.388 |