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- PDB-3a8w: Crystal Structure of PKCiota kinase domain -

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Basic information

Entry
Database: PDB / ID: 3a8w
TitleCrystal Structure of PKCiota kinase domain
ComponentsProtein kinase C iota type
KeywordsTRANSFERASE / Protein kinase C iota / kinase domain / ATP complex
Function / homology
Function and homology information


Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / protein kinase C / eye photoreceptor cell development / diacylglycerol-dependent serine/threonine kinase activity / negative regulation of glial cell apoptotic process / Schmidt-Lanterman incisure / membrane organization ...Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / protein kinase C / eye photoreceptor cell development / diacylglycerol-dependent serine/threonine kinase activity / negative regulation of glial cell apoptotic process / Schmidt-Lanterman incisure / membrane organization / cellular response to chemical stress / positive regulation of endothelial cell apoptotic process / cell-cell junction organization / establishment or maintenance of epithelial cell apical/basal polarity / tight junction / protein targeting to membrane / intercellular bridge / positive regulation of Notch signaling pathway / cell leading edge / brush border / regulation of postsynaptic membrane neurotransmitter receptor levels / bicellular tight junction / vesicle-mediated transport / positive regulation of glial cell proliferation / cytoskeleton organization / p75NTR recruits signalling complexes / response to interleukin-1 / secretion / actin filament organization / positive regulation of D-glucose import / positive regulation of protein localization to plasma membrane / Schaffer collateral - CA1 synapse / phospholipid binding / Pre-NOTCH Transcription and Translation / positive regulation of neuron projection development / cellular response to insulin stimulus / microtubule cytoskeleton / KEAP1-NFE2L2 pathway / cell migration / positive regulation of NF-kappaB transcription factor activity / negative regulation of neuron apoptotic process / protein kinase activity / intracellular signal transduction / endosome / protein phosphorylation / apical plasma membrane / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain ...Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / 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 / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Protein kinase C iota type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTakimura, T. / Kamata, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structures of the PKC-iota kinase domain in its ATP-bound and apo forms reveal defined structures of residues 533-551 in the C-terminal tail and their roles in ATP binding
Authors: Takimura, T. / Kamata, K. / Fukasawa, K. / Ohsawa, H. / Komatani, H. / Yoshizumi, T. / Takahashi, I. / Kotani, H. / Iwasawa, Y.
History
DepositionOct 11, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C iota type
B: Protein kinase C iota type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8205
Polymers79,7102
Non-polymers1,1103
Water2,918162
1
A: Protein kinase C iota type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3622
Polymers39,8551
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein kinase C iota type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4583
Polymers39,8551
Non-polymers6032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-29 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.039, 89.136, 206.395
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein kinase C iota type / nPKC-iota / Atypical protein kinase C-lambda/iota / aPKC-lambda/iota / PRKC-lambda/iota


Mass: 39854.820 Da / Num. of mol.: 2 / Fragment: UNP residues 249-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41743, protein kinase C
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: PEG3350, ammonium sulfate, pH 5.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 5, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 46755 / Num. obs: 46708 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.058 / Χ2: 1.019 / Net I/σ(I): 28.68
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.24 / Num. unique all: 4626 / Χ2: 0.969 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.92 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.87 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.301 2332 5.1 %RANDOM
Rwork0.247 ---
all0.25 46144 --
obs0.25 46144 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.06 Å2 / Biso mean: 32.472 Å2 / Biso min: 4.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2---0.36 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5369 0 67 162 5598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225568
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9817540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9285651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14824.246285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.09515956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0441535
X-RAY DIFFRACTIONr_chiral_restr0.0980.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214243
X-RAY DIFFRACTIONr_mcbond_it1.4011.53268
X-RAY DIFFRACTIONr_mcangle_it2.37525285
X-RAY DIFFRACTIONr_scbond_it3.59232300
X-RAY DIFFRACTIONr_scangle_it5.3544.52255
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 182 -
Rwork0.329 3189 -
all-3371 -
obs--99.91 %

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