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- PDB-2y0a: Structure of DAPK1 construct residues 1-304 -

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Basic information

Entry
Database: PDB / ID: 2y0a
TitleStructure of DAPK1 construct residues 1-304
ComponentsDEATH-ASSOCIATED PROTEIN KINASE 1
KeywordsTRANSFERASE / CALMODULIN / ESPRIT
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 / regulation of autophagy / negative regulation of translation / 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
Death-associated protein kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYumerefendi, H. / Mas, P.J. / Dordevic, N. / McCarthy, A.A. / Hart, D.J.
CitationJournal: To be Published
Title: Library-Based Construct Screening of Death-Associated Protein Kinase 1 Identifies the Minimal Calmodulin Interaction Region and Autoinhibitory Conformation of the Catalytic Domain
Authors: Yumerefendi, H. / Mas, P.J. / Dordevic, N. / Mccarthy, A.A. / Hart, D.J.
History
DepositionDec 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)37,4622
Polymers37,2661
Non-polymers1951
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.220, 78.880, 111.470
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 / DEATH ASSOCIATED KINASE 1 / DAP KINASE 1


Mass: 37266.348 Da / Num. of mol.: 1 / Fragment: KINASE CATALYTIC DOMAIN, RESIDUES 2-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PYUM6002/PET-9A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLAST 22 AMINO ACIDS FROM A BIOTIN ACCEPTOR TAG

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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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growpH: 6 / Details: 5% PEG 6000, 0.1M MES, PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 15, 2009 / Details: KB MIRROR SYSTEM
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14084 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.3
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.3 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0085refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IG1

1ig1


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.999 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25913 710 5 %RANDOM
Rwork0.20043 ---
obs0.20336 13382 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.968 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 12 25 2439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222476
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9693344
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5375301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5424.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15815447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1121515
X-RAY DIFFRACTIONr_chiral_restr0.1190.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211865
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 51 -
Rwork0.292 936 -
obs--97.15 %

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