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Yorodumi- PDB-1mxe: Structure of the Complex of Calmodulin with the Target Sequence o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mxe | ||||||
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Title | Structure of the Complex of Calmodulin with the Target Sequence of CaMKI | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / Calmodulin-Pepide Complex / Calmodulin / CaMKI / XRAY | ||||||
Function / homology | Function and homology information Activation of RAC1 downstream of NMDARs / positive regulation of syncytium formation by plasma membrane fusion / negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / rhabdomere ...Activation of RAC1 downstream of NMDARs / positive regulation of syncytium formation by plasma membrane fusion / negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / myosin V complex / kinetochore organization / autophagic cell death / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / : / G protein-coupled opsin signaling pathway / actin filament-based movement / Ca2+/calmodulin-dependent protein kinase / regulation of protein binding / myosin V binding / channel regulator activity / cellular response to ethanol / nucleocytoplasmic transport / calcium/calmodulin-dependent protein kinase activity / muscle cell cellular homeostasis / positive regulation of dendritic spine development / regulation of synapse organization / positive regulation of muscle cell differentiation / mitotic spindle pole / myosin heavy chain binding / centriole replication / enzyme regulator activity / centriole / positive regulation of protein export from nucleus / sensory perception of sound / positive regulation of protein serine/threonine kinase activity / mitotic spindle / positive regulation of neuron projection development / spindle / regulation of protein localization / sensory perception of smell / nervous system development / cell cortex / midbody / postsynaptic density / cell differentiation / calmodulin binding / intracellular signal transduction / cell cycle / protein phosphorylation / protein serine kinase activity / centrosome / glutamatergic synapse / calcium ion binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Clapperton, J.A. / Martin, S.R. / Smerdon, S.J. / Gamblin, S.J. / Bayley, P.M. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structure of the Complex of Calmodulin with the Target Sequence of Calmodulin-Dependent Protein Kinase I: Studies of the Kinase Activation Mechanism Authors: Clapperton, J.A. / Martin, S.R. / Smerdon, S.J. / Gamblin, S.J. / Bayley, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mxe.cif.gz | 154.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mxe.ent.gz | 122.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mxe_validation.pdf.gz | 419.2 KB | Display | wwPDB validaton report |
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Full document | 1mxe_full_validation.pdf.gz | 422.4 KB | Display | |
Data in XML | 1mxe_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1mxe_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/1mxe ftp://data.pdbj.org/pub/pdb/validation_reports/mx/1mxe | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16694.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62152 #2: Protein/peptide | Mass: 2997.628 Da / Num. of mol.: 2 / Fragment: Calmodulin Binding Domain / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: Q63450, EC: 2.7.1.123 #3: Chemical | ChemComp-CA / #4: 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: 2.11 Å3/Da / Density % sol: 41.12 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Cacodylate, Calcium chloride, MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 7.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934, 0.9500, 0.9791, 0.9794 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2002 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→30 Å / Num. all: 39543 / Num. obs: 38674 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.077 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.217 / % possible all: 100 | |||||||||||||||
Reflection | *PLUS Redundancy: 23.1 % | |||||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→29.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.168 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.112 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.529 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20 /
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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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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.188 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS |