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- PDB-1gmi: Structure of the c2 domain from novel protein kinase C epsilon -

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Basic information

Entry
Database: PDB / ID: 1gmi
TitleStructure of the c2 domain from novel protein kinase C epsilon
ComponentsPROTEIN KINASE C, EPSILON TYPE
KeywordsKINASE / PKC / C2 DOMAIN / PHOSPHOLIPIDS / PKC EPSILON.
Function / homology
Function and homology information


DAG and IP3 signaling / positive regulation of cellular glucuronidation / ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / SHC1 events in ERBB2 signaling / Role of phospholipids in phagocytosis / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / Effects of PIP2 hydrolysis / negative regulation of mitochondrial calcium ion concentration / calcium,diacylglycerol-dependent serine/threonine kinase activity ...DAG and IP3 signaling / positive regulation of cellular glucuronidation / ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / SHC1 events in ERBB2 signaling / Role of phospholipids in phagocytosis / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / Effects of PIP2 hydrolysis / negative regulation of mitochondrial calcium ion concentration / calcium,diacylglycerol-dependent serine/threonine kinase activity / positive regulation of lipid catabolic process / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / regulation of insulin secretion involved in cellular response to glucose stimulus / macrophage activation involved in immune response / regulation of release of sequestered calcium ion into cytosol / response to morphine / presynaptic cytosol / signaling receptor activator activity / negative regulation of release of sequestered calcium ion into cytosol / cellular response to ethanol / positive regulation of fibroblast migration / positive regulation of cell-substrate adhesion / positive regulation of mucus secretion / regulation of synaptic vesicle exocytosis / locomotory exploration behavior / positive regulation of wound healing / positive regulation of actin filament polymerization / positive regulation of epithelial cell migration / cellular response to platelet-derived growth factor stimulus / positive regulation of cytokinesis / negative regulation of mitochondrial membrane potential / regulation of lipid metabolic process / actin monomer binding / enzyme activator activity / regulation of peptidyl-tyrosine phosphorylation / negative regulation of protein ubiquitination / lipopolysaccharide-mediated signaling pathway / T-tubule / 14-3-3 protein binding / cell periphery / positive regulation of synaptic transmission, GABAergic / neuromuscular junction / positive regulation of insulin secretion / SH3 domain binding / cellular response to prostaglandin E stimulus / cellular response to hypoxia / peptidyl-serine phosphorylation / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / cytoskeleton / cell adhesion / intracellular signal transduction / cell cycle / cell division / Golgi membrane / signaling receptor binding / protein phosphorylation / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / mitochondrion / ATP binding / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein kinase C, epsilon / Novel protein kinase C epsilon, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Protein kinase C conserved region 2 (CalB) ...Protein kinase C, epsilon / Novel protein kinase C epsilon, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / C2 domain profile. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein kinase C epsilon type
Similarity search - Component
Biological speciesRATTUS RATTUS (black rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsOchoa, W.F. / Garcia-Garcia, J. / Fita, I. / Corbalan-Garcia, S. / Verdaguer, N. / Gomez-Fernandez, J.C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structure of the C2 Domain from Novel Protein Kinase Cepsilon. A Membrane Binding Model for Ca(2+ )-Independent C2 Domains
Authors: Ochoa, W.F. / Garcia-Garcia, J. / Fita, I. / Corbalan-Garcia, S. / Verdaguer, N. / Gomez-Fernandez, J.C.
History
DepositionSep 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN KINASE C, EPSILON TYPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2222
Polymers15,1981
Non-polymers241
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.300, 56.500, 60.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN KINASE C, EPSILON TYPE / / PROTEIN KINASE C / NPKC-EPSILON


Mass: 15198.134 Da / Num. of mol.: 1 / Fragment: C2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS RATTUS (black rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P09216
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.6
Details: 16% PEG8000, 0.1M HEPES PH=7.5, 0.2M MGCL2., pH 7.60
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
22 mg/mlDCPS1dropor DCPA
316 %(w/v)PEG80001reservoir
4100 mMHEPES1reservoir
50.2 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.993
DetectorDate: Aug 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 8248 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.1
Reflection shellHighest resolution: 1.7 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.5 / % possible all: 98
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 15661 / % possible obs: 98 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.245

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.7→20 Å / Cross valid method: 15661 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.262 -10 %
Rwork0.234 --
obs0.234 15661 98 %
Solvent computationSolvent model: DM
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 1 107 1165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 10 /
Num. reflection% reflection
Rwork1400 -
obs-90 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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