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Yorodumi- PDB-1iq5: Calmodulin/nematode CA2+/Calmodulin dependent kinase kinase fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iq5 | ||||||
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Title | Calmodulin/nematode CA2+/Calmodulin dependent kinase kinase fragment | ||||||
Components |
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Keywords | METAL BINDING PROTEIN/PROTEIN BINDING / EF-hand / CALMODULIN / PROTEIN-PEPTIDE COMPLEX / METAL BINDING PROTEIN-PROTEIN BINDING COMPLEX | ||||||
Function / homology | Function and homology information CaMK IV-mediated phosphorylation of CREB / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of RAC1 downstream of NMDARs / positive regulation of CREB transcription factor activity / Ca2+/calmodulin-dependent protein kinase / calmodulin-dependent protein kinase activity / positive regulation of protein kinase activity / calcium-mediated signaling / calmodulin binding / signaling receptor binding ...CaMK IV-mediated phosphorylation of CREB / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of RAC1 downstream of NMDARs / positive regulation of CREB transcription factor activity / Ca2+/calmodulin-dependent protein kinase / calmodulin-dependent protein kinase activity / positive regulation of protein kinase activity / calcium-mediated signaling / calmodulin binding / signaling receptor binding / protein phosphorylation / DNA-templated transcription / calcium ion binding / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kurokawa, H. / Osawa, M. / Kurihara, H. / Katayama, N. / Tokumitsu, H. / Swindells, M.B. / Kainosho, M. / Ikura, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Target-induced conformational adaptation of calmodulin revealed by the crystal structure of a complex with nematode Ca(2+)/calmodulin-dependent kinase kinase peptide Authors: Kurokawa, H. / Osawa, M. / Kurihara, H. / Katayama, N. / Tokumitsu, H. / Swindells, M.B. / Kainosho, M. / Ikura, M. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase Authors: Osawa, M. / Tokumitsu, H. / Swindells, M.B. / Kurihara, H. / Orita, M. / Shibanuma, T. / Furuya, T. / Ikura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iq5.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iq5.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 1iq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/1iq5 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/1iq5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16852.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PAS / Production host: Escherichia coli (E. coli) / References: UniProt: P62155, UniProt: P0DP33*PLUS | ||
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#2: Protein/peptide | Mass: 3198.920 Da / Num. of mol.: 1 / Fragment: CALMODULIN BINDING DOMAIN (RESIDUES 331-357) / Source method: obtained synthetically Details: This sequence occurs naturally in Caenorhabditis elegans References: UniProt: Q8T8D4, UniProt: Q3Y416*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor | ||
#3: Chemical | ChemComp-CA / #4: 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: 2.4 Å3/Da / Density % sol: 48.81 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: ammonium sulfate, citratet, sodium tartrae, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: CUSTOM-MADE / Detector: IMAGE PLATE / Date: Feb 10, 1999 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 57477 / Num. obs: 17155 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 25.798 Å2 / Rmerge(I) obs: 0.024 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.212 / % possible all: 89.1 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 57477 |
Reflection shell | *PLUS % possible obs: 89.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→100 Å / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→100 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 100 Å / Rfactor obs: 0.217 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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