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Yorodumi- PDB-4fg9: Crystal structure of human calcium/calmodulin-dependent protein k... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fg9 | ||||||
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Title | Crystal structure of human calcium/calmodulin-dependent protein kinase I 1-320 in complex with ATP | ||||||
Components | Calcium/calmodulin-dependent protein kinase type 1 | ||||||
Keywords | TRANSFERASE / CaMK / calmodulin / autoinhibition / regulation mechanism / kinase | ||||||
Function / homology | Function and homology information 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 / calcium/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 / calcium/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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Zha, M. / Zhong, C. / Ou, Y. / Wang, J. / Han, L. / Ding, J. | ||||||
Citation | Journal: Plos One / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fg9.cif.gz | 237.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fg9.ent.gz | 191.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fg9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4fg9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4fg9_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 4fg9_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/4fg9 ftp://data.pdbj.org/pub/pdb/validation_reports/fg/4fg9 | HTTPS FTP |
-Related structure data
Related structure data | 4fg7SC 4fg8C 4fgbC S: Starting model for refinement C: citing same article (ref.) |
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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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36424.559 Da / Num. of mol.: 2 / Fragment: residues 1-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK1 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q14012, Ca2+/calmodulin-dependent protein kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.5M (NH4)2SO4, 100mM tri-sodium citrate, 0.8M Li2SO4, pH 5.6, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 11, 2008 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.4→76.51 Å / Num. all: 23421 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.1 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FG7 Resolution: 2.4→76.51 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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: 168.89 Å2 / Biso mean: 43.8183 Å2 / Biso min: 15.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→76.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.398→2.46 Å / Total num. of bins used: 20
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