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- PDB-1ik7: Crystal Structure of the Uncomplexed Pelle Death Domain -

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Basic information

Entry
Database: PDB / ID: 1ik7
TitleCrystal Structure of the Uncomplexed Pelle Death Domain
ComponentsPROBABLE SERINE/THREONINE-PROTEIN KINASE Pelle
KeywordsTRANSFERASE / siNgle helix / MPD crystallization / structural transition
Function / homology
Function and homology information


determination of dorsal/ventral asymmetry / hemocyte proliferation / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' / Activated PLL kinase is autophosphorylated in the TL receptor 'signalling complex' / Phosphorylated CACT, DL and DIF homodimers dissociate from the TL receptor 'signalling complex' / PLL kinase binds to TUB in the TL receptor 'signalling complex' / positive regulation of antifungal peptide production / TAK1-dependent IKK and NF-kappa-B activation / activated TAK1 mediates p38 MAPK activation ...determination of dorsal/ventral asymmetry / hemocyte proliferation / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' / Activated PLL kinase is autophosphorylated in the TL receptor 'signalling complex' / Phosphorylated CACT, DL and DIF homodimers dissociate from the TL receptor 'signalling complex' / PLL kinase binds to TUB in the TL receptor 'signalling complex' / positive regulation of antifungal peptide production / TAK1-dependent IKK and NF-kappa-B activation / activated TAK1 mediates p38 MAPK activation / IRAK1 recruits IKK complex / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / zygotic specification of dorsal/ventral axis / Interleukin-1 signaling / positive regulation of hippo signaling / larval somatic muscle development / antifungal innate immune response / Toll signaling pathway / positive regulation of ubiquitin-dependent protein catabolic process / dorsal/ventral pattern formation / cytokine-mediated signaling pathway / positive regulation of protein catabolic process / cellular response to lipopolysaccharide / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein domain specific binding / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single helix bin / Pelle, death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain ...Single helix bin / Pelle, death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase pelle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsXiao, T. / Gardner, K.H. / Sprang, S.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Cosolvent-induced transformation of a death domain tertiary structure
Authors: Xiao, T. / Gardner, K.H. / Sprang, S.R.
History
DepositionMay 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: PROBABLE SERINE/THREONINE-PROTEIN KINASE Pelle
B: PROBABLE SERINE/THREONINE-PROTEIN KINASE Pelle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4997
Polymers24,8932
Non-polymers6075
Water34219
1
A: PROBABLE SERINE/THREONINE-PROTEIN KINASE Pelle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8094
Polymers12,4461
Non-polymers3623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROBABLE SERINE/THREONINE-PROTEIN KINASE Pelle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6913
Polymers12,4461
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.106, 95.542, 103.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein PROBABLE SERINE/THREONINE-PROTEIN KINASE Pelle / PELLE


Mass: 12446.343 Da / Num. of mol.: 2 / Fragment: Death Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pelle / Plasmid: pET15b / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05652, EC: 2.7.1.37
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 45% 2-methyl-2,4-pentanediol, Tris, 0.4 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris-Cl1droppH7.5
3100 mM1dropNaCl
41 mMdithiothreitol1drop
51 mMEDTA1drop
640-46 %MPD1reservoir
70.4-0.6 M1reservoirNaCl
80.1 MTris-Cl1reservoirpH8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F110.947
SYNCHROTRONCHESS F120.947
SYNCHROTRONCHESS F230.9795, 0.9791, 0.9789, 0.9778
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDFeb 10, 2000mirrors
ADSC QUANTUM 42CCDFeb 10, 2000mirrors
ADSC QUANTUM 43CCDFeb 10, 2000mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2YALE MIRRORSSINGLE WAVELENGTHMx-ray1
3crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9471
20.97951
30.97911
40.97891
50.97781
ReflectionResolution: 2.3→25 Å / Num. all: 15711 / Num. obs: 15711 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 19.6
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 4 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3 / Num. unique all: 1022 / Rsym value: 0.256 / % possible all: 99.8
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.3→24.79 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 361892.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: maximum likelihood refinement target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1550 10.2 %RANDOM
Rwork0.239 ---
all0.268 15711 --
obs0.239 15265 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.12 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 55.9 Å2
Baniso -1Baniso -2Baniso -3
1-18.55 Å20 Å20 Å2
2---9.9 Å20 Å2
3----8.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms848 0 32 27 907
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d17
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 240 9.9 %
Rwork0.264 2181 -
obs-1800 94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3MPD.PARAMMPD.TOP
X-RAY DIFFRACTION4TRS.PARAMTRS.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 25 Å / % reflection Rfree: 10 % / Rfactor all: 0.268 / Rfactor obs: 0.239 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.84
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.308 / Rfactor Rwork: 0.264

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