+Open data
-Basic information
Entry | Database: PDB / ID: 1a25 | ||||||
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Title | C2 DOMAIN FROM PROTEIN KINASE C (BETA) | ||||||
Components | PROTEIN KINASE C (BETA) | ||||||
Keywords | CALCIUM-BINDING PROTEIN / CALCIUM++/PHOSPHOLIPID BINDING PROTEIN | ||||||
Function / homology | Function and homology information dibenzo-p-dioxin metabolic process / Depolymerization of the Nuclear Lamina / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / Activation of NF-kappaB in B cells / histone H3T6 kinase activity / VEGFR2 mediated cell proliferation / positive regulation of odontogenesis of dentin-containing tooth / positive regulation of B cell receptor signaling pathway / spectrin ...dibenzo-p-dioxin metabolic process / Depolymerization of the Nuclear Lamina / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / Activation of NF-kappaB in B cells / histone H3T6 kinase activity / VEGFR2 mediated cell proliferation / positive regulation of odontogenesis of dentin-containing tooth / positive regulation of B cell receptor signaling pathway / spectrin / regulation of glucose transmembrane transport / WNT5A-dependent internalization of FZD4 / RHO GTPases Activate NADPH Oxidases / protein kinase C / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / negative regulation of glucose transmembrane transport / cellular response to carbohydrate stimulus / diacylglycerol-dependent serine/threonine kinase activity / response to vitamin D / presynaptic cytosol / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of growth / regulation of synaptic vesicle exocytosis / nuclear androgen receptor binding / regulation of dopamine secretion / B cell activation / Trafficking of GluR2-containing AMPA receptors / calyx of Held / calcium channel regulator activity / response to glucose / negative regulation of insulin receptor signaling pathway / presynaptic modulation of chemical synaptic transmission / post-translational protein modification / nuclear receptor coactivator activity / protein kinase C binding / brush border membrane / B cell receptor signaling pathway / positive regulation of insulin secretion / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / presynapse / histone binding / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / adaptive immune response / intracellular signal transduction / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / apoptotic process / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sutton, R.B. / Sprang, S.R. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Structure of the protein kinase Cbeta phospholipid-binding C2 domain complexed with Ca2+. Authors: Sutton, R.B. / Sprang, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a25.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a25.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 1a25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/1a25 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/1a25 | HTTPS FTP |
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-Related structure data
Related structure data | 1rsyS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.912012, 0.409902, -0.014639), Vector: |
-Components
#1: Protein | Mass: 16882.111 Da / Num. of mol.: 2 / Fragment: CALCIUM/PHOSPHOLIPID BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Plasmid: PGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P68403, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-PSE / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 15% PEG1500, 100 MM MES, PH 6.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 6.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 133 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Oct 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 12297 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.083 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.7→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 8 / Rsym value: 0.26 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RSY Resolution: 2.7→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1365552.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: REFINEMENT TARGET FUNCTION : MLF DATA CUTOFF HIGH (ABS(F)) : 1365552.04 DATA CUTOFF LOW (ABS(F)) : 0.000000
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.345 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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