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- PDB-3dgk: Crystal structure of a glycine-rich loop mutant of the death asso... -

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Basic information

Entry
Database: PDB / ID: 3dgk
TitleCrystal structure of a glycine-rich loop mutant of the death associated protein kinase catalytic domain
ComponentsDeath-associated protein kinase 1
KeywordsTRANSFERASE / Kinase domain / glycine-rich loop mutation / ANK repeat / Apoptosis / ATP-binding / Calmodulin-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
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 / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / negative regulation of translation / postsynaptic density / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein kinase activity / 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
Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMcNamara, L.K. / Schavocky, J.P. / Watterson, D.M. / Brunzelle, J.S.
CitationJournal: To be Published
Title: High resolution crystal structures of the death associated protein kinase catalytic domain with a key point mutation in the glycine-rich loop
Authors: McNamara, L.K. / Schavocky, J.P. / Watterson, D.M. / Brunzelle, J.S.
History
DepositionJun 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 27, 2016Group: Structure summary
Revision 1.3Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death-associated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)33,9271
Polymers33,9271
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.208, 62.441, 88.576
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: 33926.613 Da / Num. of mol.: 1 / Fragment: Protein kinase catalytic domain / Mutation: Q23K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK1, DAPK / Plasmid: pASK-IBA-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.92 Å3/Da / Density % sol: 36.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris pH 7.5, 0.8 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 30, 2006 / Details: Mirror
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 28268 / Num. obs: 28268 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2682 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1jks

1jks


Resolution: 1.7→25.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.112 / SU ML: 0.071 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21999 1431 5.1 %RANDOM
Rwork0.17292 ---
obs0.17534 26817 95.83 %-
all-26817 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.727 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 0 221 2450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222359
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9673207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.485296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25124.732112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16815420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4531512
X-RAY DIFFRACTIONr_chiral_restr0.110.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021807
X-RAY DIFFRACTIONr_nbd_refined0.2310.21059
X-RAY DIFFRACTIONr_nbtor_refined0.310.21663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2169
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.232
X-RAY DIFFRACTIONr_mcbond_it1.1521.51486
X-RAY DIFFRACTIONr_mcangle_it1.79822355
X-RAY DIFFRACTIONr_scbond_it2.9773979
X-RAY DIFFRACTIONr_scangle_it4.6154.5852
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 81 -
Rwork0.226 1902 -
obs--92.19 %

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