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- PDB-4uv0: Structure of a semisynthetic phosphorylated DAPK -

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Basic information

Entry
Database: PDB / ID: 4uv0
TitleStructure of a semisynthetic phosphorylated DAPK
ComponentsDEATH-ASSOCIATED PROTEIN KINASE 1
KeywordsTRANSFERASE / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / NATIVE CHEMICAL LIGATION / CALMODULIN-BINDING / NUCLEOTIDE-BINDING / APOPTOSIS
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 / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : ...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 / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / apoptotic signaling pathway / regulation of autophagy / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / negative regulation of translation / postsynaptic density / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / GTP binding / apoptotic process / 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 / 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 / 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: 2.49 Å
Authorsde Diego, I. / Rios, P. / Meyer, C. / Koehn, M. / Wilmanns, M.
CitationJournal: To be Published
Title: Molecular Mechanisms Behind Dapk Regulation: How the Phosphorylation Activity Switch Works
Authors: Temmerman, K. / Mertens, H. / Rios, P. / Simon, B. / Huart, A.S. / Piljic, A. / De Diego, I. / Svergun, D. / Schultz, C. / Koehn, M. / Wilmanns, M.
History
DepositionAug 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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)37,3212
Polymers37,1711
Non-polymers1501
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.559, 78.002, 108.861
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: 37170.691 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-321 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SEMISYNTHETIC PHOSPHOPROTEIN OBTAINED BY INTEIN-MEDIATED NATIVE CHEMICAL LIGATION. PHOSPHORYLATED IN SER308
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 5MM HEPES, 30 MM NACL, 10 MM NA2SO4,0.5 MMDTT,25% (W/V) PEGMME2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→45.1 Å / Num. obs: 15176 / % possible obs: 98.9 % / Observed criterion σ(I): 2.2 / Redundancy: 4.9 % / Biso Wilson estimate: 40.65 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.9
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 5 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.2 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W4J

2w4j


Resolution: 2.49→45.105 Å / SU ML: 0.34 / σ(F): 0.03 / Phase error: 22.65 / Stereochemistry target values: ML
Details: DISORDERED SIDE CHAINS AND REGIONS WERE EXCLUDED FROM THE MODEL. PHOPHO SER308 IS LOCATED IN DISORDERED REGIONS.
RfactorNum. reflection% reflection
Rfree0.2425 726 5.1 %
Rwork0.1931 --
obs0.1958 14240 92.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.895 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.9543 Å20 Å20 Å2
2--6.6896 Å20 Å2
3---0.2647 Å2
Refinement stepCycle: LAST / Resolution: 2.49→45.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 10 91 2462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082418
X-RAY DIFFRACTIONf_angle_d1.083266
X-RAY DIFFRACTIONf_dihedral_angle_d18.293883
X-RAY DIFFRACTIONf_chiral_restr0.073366
X-RAY DIFFRACTIONf_plane_restr0.004421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4902-2.68250.28061070.22932358X-RAY DIFFRACTION82
2.6825-2.95240.26821490.20862608X-RAY DIFFRACTION92
2.9524-3.37950.2791480.20312710X-RAY DIFFRACTION94
3.3795-4.25730.22021530.172864X-RAY DIFFRACTION98
4.2573-45.11220.22431690.18782974X-RAY DIFFRACTION97

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