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- PDB-4fg7: Crystal structure of human calcium/calmodulin-dependent protein k... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fg7 | ||||||
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Title | Crystal structure of human calcium/calmodulin-dependent protein kinase I 1-293 in complex with ATP | ||||||
![]() | Calcium/calmodulin-dependent protein kinase type 1 | ||||||
![]() | TRANSFERASE / CaMK / calmodulin / autoinhibition / regulation mechanism / kinase | ||||||
Function / homology | ![]() positive regulation of syncytium formation by plasma membrane fusion / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / Ca2+/calmodulin-dependent protein kinase / regulation of protein binding / nucleocytoplasmic transport / calmodulin-dependent protein kinase activity / Activation of RAC1 downstream of NMDARs / positive regulation of dendritic spine development / positive regulation of muscle cell differentiation ...positive regulation of syncytium formation by plasma membrane fusion / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / Ca2+/calmodulin-dependent protein kinase / regulation of protein binding / nucleocytoplasmic transport / calmodulin-dependent protein kinase activity / Activation of RAC1 downstream of NMDARs / positive regulation of dendritic spine development / positive regulation of muscle cell differentiation / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of protein export from nucleus / negative regulation of protein binding / positive regulation of protein serine/threonine kinase activity / positive regulation of neuron projection development / regulation of protein localization / nervous system development / cell differentiation / calmodulin binding / intracellular signal transduction / cell cycle / protein phosphorylation / protein serine kinase activity / signal transduction / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zha, M. / Zhong, C. / Ou, Y. / Wang, J. / Han, L. / Ding, J. | ||||||
![]() | ![]() Title: Crystal structures of human CaMKIalpha reveal insights into the regulation mechanism of CaMKI. Authors: Zha, M. / Zhong, C. / Ou, Y. / Han, L. / Wang, J. / Ding, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.9 KB | Display | ![]() |
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PDB format | ![]() | 89.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 781.2 KB | Display | ![]() |
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Full document | ![]() | 783.1 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fg8C ![]() 4fg9C ![]() 4fgbC ![]() 1a06S C: citing same article ( S: Starting model for refinement |
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Similar 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: 33203.660 Da / Num. of mol.: 1 / Fragment: residues 1-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q14012, Ca2+/calmodulin-dependent protein kinase |
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#2: Chemical | ChemComp-ATP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 200mM NH4Ac, 100mM (CH3)2AsO2Na, 25% PEG 8000, pH 6.0, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→59.46 Å / Num. all: 8967 / % possible obs: 99.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A06 Resolution: 2.7→59.46 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
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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 max: 117.41 Å2 / Biso mean: 51.0192 Å2 / Biso min: 25.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→59.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.699→2.769 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 129.3778 Å / Origin y: -22.3634 Å / Origin z: 24.2949 Å
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