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Yorodumi- PDB-3dyq: human phosphodiestrase 9 (inhibited by omitting divalent cation) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dyq | ||||||
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Title | human phosphodiestrase 9 (inhibited by omitting divalent cation) in complex with cGMP | ||||||
Components | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | ||||||
Keywords | HYDROLASE / PHOSPHODIESTERASE / ENZYME MECHANISM / cGMP / Manganese / Metal-binding / Phosphoprotein | ||||||
Function / homology | Function and homology information cGMP metabolic process / negative regulation of neural precursor cell proliferation / 3',5'-cyclic-GMP phosphodiesterase / positive regulation of cardiac muscle hypertrophy / cGMP catabolic process / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling ...cGMP metabolic process / negative regulation of neural precursor cell proliferation / 3',5'-cyclic-GMP phosphodiesterase / positive regulation of cardiac muscle hypertrophy / cGMP catabolic process / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / positive regulation of long-term synaptic potentiation / sarcolemma / ruffle membrane / perikaryon / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / signal transduction / nucleoplasm / identical protein binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Liu, S. / Mansour, M.N. / Dillman, K. / Perez, J. / Danley, D. / Menniti, F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Structural basis for the catalytic mechanism of human phosphodiesterase 9. Authors: Liu, S. / Mansour, M.N. / Dillman, K.S. / Perez, J.R. / Danley, D.E. / Aeed, P.A. / Simons, S.P. / Lemotte, P.K. / Menniti, F.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dyq.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dyq.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 3dyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dyq_validation.pdf.gz | 850.5 KB | Display | wwPDB validaton report |
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Full document | 3dyq_full_validation.pdf.gz | 859.5 KB | Display | |
Data in XML | 3dyq_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 3dyq_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/3dyq ftp://data.pdbj.org/pub/pdb/validation_reports/dy/3dyq | HTTPS FTP |
-Related structure data
Related structure data | 3dy8C 3dylC 3dynC 3dysC 1tbm C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
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-Components
#1: Protein | Mass: 38862.926 Da / Num. of mol.: 2 / Fragment: Catalytic domain, UNP residues 242-566 Source method: isolated from a genetically manipulated source Details: N-His tag (removed after purification) catalytic domain Source: (gene. exp.) Homo sapiens (human) / Gene: PDE9A / Production host: Escherichia coli (E. coli) References: UniProt: O76083, 3',5'-cyclic-GMP phosphodiesterase #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-PCG / | #4: Chemical | ChemComp-IBM / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.66 Å3/Da / Density % sol: 73.58 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 65299 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 23 |
-Processing
Software | Name: REFMAC / Version: 5.3.0008 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1TBM 1tbm Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 14.204 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.206 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.023 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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