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- PDB-6qmo: Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regu... -

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Basic information

Entry
Database: PDB / ID: 6qmo
TitleDeath-associated Protein Kinase 1 (DAPK1) catalytic and auto-regulatory domains with S289E and S308A mutations
ComponentsDeath-associated protein kinase 1
KeywordsSIGNALING PROTEIN / kinase / apoptosis / autophagy / CaMK
Function / homology
Function and homology information


cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / protein autophosphorylation / regulation of apoptotic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / calmodulin binding / postsynaptic density / negative regulation of translation / regulation of autophagy / intracellular signal transduction / protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / GTP binding / glutamatergic synapse / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHuart, A.-S. / Wilmanns, M.
CitationJournal: To Be Published
Title: Molecular mechanisms behind DAPK regulation: how phosphorylation switches work
Authors: Huart, A.-S. / Simon, B. / Lubner, J. / Mertens, H.D.T. / Temmerman, K. / Hoffmann, J.-E. / Svergun, D.I. / Schwartz, D. / Schultz, C. / Wilmanns, M.
History
DepositionFeb 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,87213
Polymers35,9921
Non-polymers88012
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-32 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.207, 75.752, 93.960
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 Death-associated protein kinase 1 / DAP kinase 1


Mass: 35992.215 Da / Num. of mol.: 1 / Mutation: S289E S308A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK1, DAPK / Production host: Escherichia coli (E. coli)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.32 Å3/Da / Density % sol: 47.01 % / Description: plate needle
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2016 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.81→47.21 Å / Num. obs: 31119 / % possible obs: 98.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.051 / Rrim(I) all: 0.133 / Net I/σ(I): 9.3
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.242 / Rpim(I) all: 0.457 / Rrim(I) all: 1.193 / % possible all: 97.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
AimlessCCP4i2 v 0.0.5data scaling
Coot0.8.6model building
REFMACCCP4i2 v 0.0.5refinement
PHENIX1.9-1692refinement
PHASER1.9-1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B4L

4b4l


Resolution: 1.87→42.182 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 22.2
RfactorNum. reflection% reflection
Rfree0.2236 1414 5 %
Rwork0.1859 --
obs0.1878 28280 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→42.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 51 115 2592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082553
X-RAY DIFFRACTIONf_angle_d0.8333433
X-RAY DIFFRACTIONf_dihedral_angle_d6.2822162
X-RAY DIFFRACTIONf_chiral_restr0.06371
X-RAY DIFFRACTIONf_plane_restr0.006444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.93690.33141440.2922636X-RAY DIFFRACTION99
1.9369-2.01440.27621270.25772611X-RAY DIFFRACTION98
2.0144-2.10610.28361390.22362617X-RAY DIFFRACTION98
2.1061-2.21710.27231340.19492660X-RAY DIFFRACTION99
2.2171-2.3560.22111310.18362681X-RAY DIFFRACTION99
2.356-2.53790.2321510.18332641X-RAY DIFFRACTION99
2.5379-2.79320.22811410.17062699X-RAY DIFFRACTION99
2.7932-3.19730.20291370.16572707X-RAY DIFFRACTION99
3.1973-4.02780.21091490.15562744X-RAY DIFFRACTION100
4.0278-42.19310.19931610.18972870X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.61-0.1660.12280.7651-0.24550.49320.0410.1620.1704-0.1591-0.04370.06140.06420.09750.0030.2072-0.0015-0.03280.18120.04360.1864-7.693619.6189-17.1294
20.43560.8237-0.3950.8555-0.04481.0780.0328-0.0070.0013-0.0436-0.1101-0.02950.0947-0.0505-0.0060.13520.0257-0.02310.1478-0.00290.1561-17.6755.1794-6.5816
30.92020.3092-0.17780.78160.06760.67790.0514-0.0379-0.17870.2133-0.06590.11210.4749-0.17430.00150.3087-0.0063-0.0210.18790.00720.1976-24.2426-7.4819-2.4597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 4 through 87 )
2X-RAY DIFFRACTION2chain A and (resid 88 through 212 )
3X-RAY DIFFRACTION3chain A and (resid 213 through 302 )

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