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- PDB-1jkt: TETRAGONAL CRYSTAL FORM OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED... -

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Basic information

Entry
Database: PDB / ID: 1jkt
TitleTETRAGONAL CRYSTAL FORM OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE
ComponentsDEATH-ASSOCIATED PROTEIN KINASE
KeywordsTRANSFERASE
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 / syntaxin-1 binding / calcium/calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...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 / syntaxin-1 binding / calcium/calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / postsynaptic density / calmodulin binding / non-specific serine/threonine protein kinase / negative regulation of translation / 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 / 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) ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / 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 / Resolution: 3.5 Å
AuthorsTereshko, V. / Teplova, M. / Brunzelle, J. / Watterson, D.M. / Egli, M.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structures of the catalytic domain of human protein kinase associated with apoptosis and tumor suppression.
Authors: Tereshko, V. / Teplova, M. / Brunzelle, J. / Watterson, D.M. / Egli, M.
History
DepositionJul 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEATH-ASSOCIATED PROTEIN KINASE
B: DEATH-ASSOCIATED PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)67,5892
Polymers67,5892
Non-polymers00
Water00
1
A: DEATH-ASSOCIATED PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)33,7941
Polymers33,7941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DEATH-ASSOCIATED PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)33,7941
Polymers33,7941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.370, 58.370, 212.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein DEATH-ASSOCIATED PROTEIN KINASE / DAP KINASE 1


Mass: 33794.367 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, PROTEIN KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P53355, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
220 MTris-HCl1droppH7.5
31 mMdithiothreitol1drop
41 mMEDTA1drop
50.1 M1dropNaCl
65 %(w/v)PEG10001reservoir
740 %(v/v)PEG3001reservoir
80.1Tris-HCl1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 8704 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 3.5→4 Å / Rmerge(I) obs: 0.39 / % possible all: 89.2
Reflection
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Lowest resolution: 4 Å / % possible obs: 96.1 % / Num. unique obs: 892 / Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.5→58.72 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.829 / SU B: 37.981 / SU ML: 0.626 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.786 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29679 903 10.6 %RANDOM
Rwork0.27174 ---
obs0.27286 8255 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.824 Å2
Baniso -1Baniso -2Baniso -3
1-4.8 Å20 Å20 Å2
2--4.8 Å20 Å2
3----9.61 Å2
Refinement stepCycle: LAST / Resolution: 3.5→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4468 0 0 0 4468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224564
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1461.9626166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9043550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.39715874
X-RAY DIFFRACTIONr_chiral_restr0.1210.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023426
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3840.33113
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2750.5416
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3710.371
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1661.52750
X-RAY DIFFRACTIONr_mcangle_it2.16424466
X-RAY DIFFRACTIONr_scbond_it2.76931814
X-RAY DIFFRACTIONr_scangle_it4.7154.51700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.576 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 38
Rwork0.312 563
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)
10.5572-0.1869-0.23171.6355-0.71691.48750.12730.18570.207-0.2137-0.0456-0.02760.16830.0774-0.08170.23420.0844-0.07650.2395-0.03050.3206-22.191740.352811.713
20.50420.09030.44980.6907-0.20592.9909-0.1006-0.11290.11540.0298-0.014-0.034-0.1379-0.1270.11470.12320.0565-0.05780.08030.00750.23361.687510.7644-0.328
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2761 - 275
2X-RAY DIFFRACTION2BB2 - 2761 - 275
Refinement
*PLUS
Rfactor obs: 0.273 / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.272
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.69
LS refinement shell
*PLUS
Rfactor Rfree: 0.361 / Rfactor Rwork: 0.312

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