+Open data
-Basic information
Entry | Database: PDB / ID: 5kjx | ||||||||||||
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Title | Co-crystal Structure of PKA RI alpha CNB-B domain with cAMP | ||||||||||||
Components | cAMP-dependent protein kinase type I-alpha regulatory subunitCAMP-dependent pathway | ||||||||||||
Keywords | SIGNALING PROTEIN / Cyclic nucleotide / cAMP-dependent protein kinase / Nucleotide selectivity / Cyclic nucleotide binding domain | ||||||||||||
Function / homology | Function and homology information sperm connecting piece / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / ALK mutants bind TKIs / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / sarcomere organization / cardiac muscle cell proliferation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation ...sperm connecting piece / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / ALK mutants bind TKIs / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / sarcomere organization / cardiac muscle cell proliferation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / cAMP-dependent protein kinase complex / cellular response to glucagon stimulus / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / mesoderm formation / Signaling by ALK fusions and activated point mutants / DARPP-32 events / Hedgehog 'off' state / cAMP binding / multivesicular body / FCGR3A-mediated IL10 synthesis / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / intracellular signal transduction / protein domain specific binding / negative regulation of gene expression / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / protein-containing complex / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Lorenz, R. / Moon, E. / Kim, J.J. / Huang, G.Y. / Kim, C. / Herberg, F.W. | ||||||||||||
Funding support | Germany, United States, 3items
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Citation | Journal: Biochem. J. / Year: 2017 Title: Mutations of PKA cyclic nucleotide-binding domains reveal novel aspects of cyclic nucleotide selectivity. Authors: Lorenz, R. / Moon, E.W. / Kim, J.J. / Schmidt, S.H. / Sankaran, B. / Pavlidis, I.V. / Kim, C. / Herberg, F.W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kjx.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kjx.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 5kjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/5kjx ftp://data.pdbj.org/pub/pdb/validation_reports/kj/5kjx | HTTPS FTP |
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-Related structure data
Related structure data | 5kjyC 5kjzC 1rgsS 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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Unit cell |
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Details | monomer according to gel filtration |
-Components
#1: Protein | Mass: 16956.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR1A, PKR1, PRKAR1, TSE1 / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): TP2000 (delta cya) / References: UniProt: P10644 |
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#2: Chemical | ChemComp-CMP / |
#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: 2.18 Å3/Da / Density % sol: 43.64 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% w/v PEG 8000, 100mM imidazole/hydrochloric acid pH 6.5, 3% v/v MPD |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→24.65 Å / Num. obs: 11873 / % possible obs: 97.08 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 50.71 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.5 / % possible all: 74.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RGS Resolution: 1.9→24.646 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.77
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Bsol: 34.299 Å2 / ksol: 0.291 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.646 Å
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Refine LS restraints |
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LS refinement shell |
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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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