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- PDB-2yaa: Crystal structure of the autoinhibited form of mouse DAPK2 in com... -

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Basic information

Entry
Database: PDB / ID: 2yaa
TitleCrystal structure of the autoinhibited form of mouse DAPK2 in complex with ATP
ComponentsDEATH-ASSOCIATED PROTEIN KINASE 2
KeywordsTRANSFERASE / APOPTOSIS
Function / homology
Function and homology information


autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / cytoplasmic vesicle / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / protein phosphorylation / protein serine kinase activity ...autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / cytoplasmic vesicle / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / apoptotic process / ATP binding / cytoplasm
Similarity search - Function
Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Death-associated protein kinase 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPatel, A.K. / Kursula, P.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure of the Dimeric Autoinhibited Conformation of Dapk2, a Pro-Apoptotic Protein Kinase.
Authors: Patel, A.K. / Yadav, R.P. / Majava, V. / Kursula, I. / Kursula, P.
History
DepositionFeb 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: DEATH-ASSOCIATED PROTEIN KINASE 2
B: DEATH-ASSOCIATED PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8387
Polymers83,5922
Non-polymers1,2475
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-41.8 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.100, 86.020, 124.420
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 2 / DAP KINASE 2 / DAP-KINASE-RELATED PROTEIN 1 / DRP-1


Mass: 41795.848 Da / Num. of mol.: 2 / Fragment: RESIDUES 11-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PTH27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS RARE
References: UniProt: Q8VDF3, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.02 Å3/Da / Density % sol: 39.1 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 30082 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 28.21 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A2A

2a2a


Resolution: 2.3→29.855 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 30.27 / Stereochemistry target values: ML
Details: THE C-TERMINAL 59 RESIDUES ARE NOT VISIBLE IN ELECTRON DENSITY, MOST LIKELY THE C-TERMINAL TAIL HAS DEGRADED DURING CRYSTALLIZATION.
RfactorNum. reflection% reflection
Rfree0.2707 1496 5 %
Rwork0.2158 --
obs0.2186 30065 97.56 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.4901 Å20 Å20 Å2
2--18.5135 Å20 Å2
3---2.7873 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 73 352 5286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045063
X-RAY DIFFRACTIONf_angle_d0.7676852
X-RAY DIFFRACTIONf_dihedral_angle_d16.6531920
X-RAY DIFFRACTIONf_chiral_restr0.049766
X-RAY DIFFRACTIONf_plane_restr0.002871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2999-2.38210.31191480.23662834X-RAY DIFFRACTION98
2.3821-2.47740.36071470.23152859X-RAY DIFFRACTION99
2.4774-2.59010.31221550.23552838X-RAY DIFFRACTION99
2.5901-2.72660.36261500.22742870X-RAY DIFFRACTION99
2.7266-2.89730.30091520.23452858X-RAY DIFFRACTION99
2.8973-3.12080.32651500.22882868X-RAY DIFFRACTION99
3.1208-3.43440.31481500.22832850X-RAY DIFFRACTION98
3.4344-3.93040.25711330.22212710X-RAY DIFFRACTION92
3.9304-4.94830.20731490.18092833X-RAY DIFFRACTION95
4.9483-29.8570.20611620.19953049X-RAY DIFFRACTION98
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)
10.0260.0036-0.02170.0459-0.0340.0472-0.03930.0178-0.0091-0.0527-0.03620.02610.0208-0.0058-0.05410.13080.06390.0130.06030.00940.1502-13.2664-15.4929-32.2325
20.0077-0.0117-0.0160.13990.01410.02120.09090.05370.0622-0.17280.00810.0143-0.0978-0.00710.00450.15870.0319-0.01430.195-0.01380.2146-13.6578-2.909-36.1821
30.0628-0.004-0.0390.04280.00860.0673-0.00480.00350.0086-0.03060.0130.07080.03550.06470.00670.034-0.00990.00220.05440.00760.0486-22.1714-0.4156-22.0651
40.11180.0390.04190.04530.00040.03280.0152-0.06710.09360.0397-0.01670.036-0.0358-0.0771-0.07650.0372-0.02370.03650.07710.00010.0468-34.159610.8409-20.5821
50.00550.0029-0.0110.0114-0.01610.02730.0434-0.03530.0440.08490.0894-0.0372-0.0317-0.06480.00410.1761-0.03590.00890.164-0.03190.2004-48.9616-16.5292-49.9073
60.04-0.0263-0.01010.02840.00010.00410.0438-0.110.00860.10250.08-0.05940.0025-0.03330.01380.1507-0.0418-0.03360.1212-0.02050.0652-48.8091-6.2748-45.4632
70.07250.07750.0550.08110.06240.0422-0.00110.0792-0.0792-0.04490.0646-0.06130.00590.03080.03040.1057-0.00190.02550.13150.02440.0869-42.567-3.3761-62.0642
80.1471-0.02790.03230.0106-0.01760.0671-0.0263-0.0890.05310.02440.0127-0.0046-0.04-0.0168-0.09360.03330.0393-0.05370.035-0.0766-0.0953-40.81412.3795-56.4901
90.4135-0.10760.16910.0884-0.05150.1350.01460.32320.047-0.0489-0.0154-0.1157-0.07930.1726-0.0417-0.0447-0.0220.1020.15670.03270.0125-28.744410.9742-63.5755
100.0049-0.00870.01260.0143-0.02120.0314-0.00580.02390.0142-0.02050.00040.02660.0041-0.0125-0.0040.22610.1376-0.11790.2605-0.04180.2857-23.0882-7.2364-30.5841
110.01240.01390.02530.04410.06390.09570.0009-0.01520.00090.0174-0.0045-0.015-0.0090.0020.00050.1416-0.0035-0.11060.2401-0.00730.096-39.3755-8.4332-53.2791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 2:45
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 46:84
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 85:174
4X-RAY DIFFRACTION4CHAIN A AND RESSEQ 175:301
5X-RAY DIFFRACTION5CHAIN B AND RESSEQ 3:32
6X-RAY DIFFRACTION6CHAIN B AND RESSEQ 33:70
7X-RAY DIFFRACTION7CHAIN B AND RESSEQ 71:133
8X-RAY DIFFRACTION8CHAIN B AND RESSEQ 134:183
9X-RAY DIFFRACTION9CHAIN B AND RESSEQ 184:301
10X-RAY DIFFRACTION10CHAIN A AND RESID 1302
11X-RAY DIFFRACTION11CHAIN B AND RESID 1302

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