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- PDB-7v0g: Structure of cAMP-dependent protein kinase using a MD-MX procedur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7v0g | ||||||
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Title | Structure of cAMP-dependent protein kinase using a MD-MX procedure, produced using 1.63 Angstrom data | ||||||
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Function / homology | ![]() spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wych, D.C. / Aoto, P.C. / Wall, M.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular-dynamics simulation methods for macromolecular crystallography. Authors: Wych, D.C. / Aoto, P.C. / Vu, L. / Wolff, A.M. / Mobley, D.L. / Fraser, J.S. / Taylor, S.S. / Wall, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.5 KB | Display | ![]() |
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PDB format | ![]() | 210.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ujxC ![]() 3fjqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules EI
#1: Protein | ![]() Mass: 40737.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | ![]() Mass: 2111.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Residues 5-23 of the PKA-C inhibitor PKI / Source: (synth.) ![]() ![]() |
-Non-polymers , 4 types, 500 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
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#3: Chemical | ChemComp-ADP / ![]() | ||||
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#4: Chemical | ![]() #5: Chemical | #6: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.75 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 4000, 0.05 M MES pH 5.2, 0.05 M MgCl2, and 0.005 M DTT |
-Data collection
Diffraction | Mean temperature: 285 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2018 Details: Primary Mirror: Flat; Secondary Mirror: uncooled cyllindrical silicon bent into torroid; 2:1 demagnification; Both mirrors coated with Pt/Rh |
Radiation | Monochromator: Water-cooled flat double Si(111) Khozu monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.63→47.42 Å / Num. obs: 58663 / % possible obs: 99.47 % / Redundancy: 4.6 % / Biso Wilson estimate: 19.77 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1056 / Rpim(I) all: 0.0534 / Rrim(I) all: 0.1188 / Net I/av σ(I): 7.39 / Net I/σ(I): 7.39 |
Reflection shell | Resolution: 1.63→1.688 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.374 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 5770 / CC1/2: 0.529 / CC star: 0.832 / Rpim(I) all: 0.6996 / Rrim(I) all: 0.1188 / % possible all: 99.79 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3FJQ Resolution: 1.63→42.07 Å / SU ML: 0.1774 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.2502 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→42.07 Å
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Refine LS restraints |
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LS refinement shell |
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