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Open data
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Basic information
Entry | Database: PDB / ID: 2vfy | ||||||
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Title | AKAP18 delta central domain | ||||||
![]() | AKAP18 DELTA | ||||||
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Function / homology | Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gold, M.G. / Smith, F.D. / Scott, J.D. / Barford, D. | ||||||
![]() | ![]() Title: Akap18 Contains a Phosphoesterase Domain that Binds AMP Authors: Gold, M.G. / Smith, F.D. / Scott, J.D. / Barford, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.4 KB | Display | ![]() |
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PDB format | ![]() | 38.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 23226.936 Da / Num. of mol.: 1 / Fragment: RESIDUES 88-292 Source method: isolated from a genetically manipulated source Details: 2H PHOSPHOESTERASE DOMAIN / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow![]() | pH: 7.5 / Details: 0.1 M TRIS HCL PH 8, 10 % PEG 8K, 7 MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 30, 2005 / Details: MIRRORS |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→97.13 Å / Num. obs: 18073 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 2.73 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.71 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: NONE Resolution: 1.8→97.13 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.656 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.137 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→97.13 Å
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Refine LS restraints |
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