+Open data
-Basic information
Entry | Database: PDB / ID: 3dyn | ||||||
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Title | human phosphodiestrase 9 in complex with cGMP (Zn inhibited) | ||||||
Components | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | ||||||
Keywords | HYDROLASE / phophodiestrase / 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 / ruffle membrane / sarcolemma / perikaryon / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / endoplasmic reticulum / 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: 2.1 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 | 3dyn.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dyn.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dyn_validation.pdf.gz | 811.6 KB | Display | wwPDB validaton report |
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Full document | 3dyn_full_validation.pdf.gz | 820.2 KB | Display | |
Data in XML | 3dyn_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 3dyn_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/3dyn ftp://data.pdbj.org/pub/pdb/validation_reports/dy/3dyn | HTTPS FTP |
-Related structure data
Related structure data | 3dy8C 3dylC 3dyqC 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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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: A B) |
-Components
-Protein , 1 types, 2 molecules AB
#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) catalytic domain / Source: (gene. exp.) Homo sapiens (human) / Gene: PDE9A / Production host: Escherichia coli (E. coli) References: UniProt: O76083, 3',5'-cyclic-GMP phosphodiesterase |
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-Non-polymers , 5 types, 457 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IBM / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.69 Å3/Da / Density % sol: 73.75 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 87053 / Num. obs: 77963 / % possible obs: 99.82 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.1 |
-Processing
Software | Name: REFMAC / Version: 5.3.0008 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1TBM 1tbm Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.496 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / 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: 31.797 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.156 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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