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- PDB-2ya9: Crystal structure of the autoinhibited form of mouse DAPK2 -

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Basic information

Entry
Database: PDB / ID: 2ya9
TitleCrystal structure of the autoinhibited form of mouse DAPK2
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 / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity ...autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / cytoplasmic vesicle / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
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. ...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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(4S,5S)-1,2-DITHIANE-4,5-DIOL / 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 1.1Nov 2, 2011Group: Database references / Version format compliance
Revision 1.2Dec 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)83,9365
Polymers83,5922
Non-polymers3453
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-12.6 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.040, 86.440, 124.270
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-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.06 Å3/Da / Density % sol: 40.21 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 30489 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 24.35 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.6 / % 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→40.822 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 31.19 / Stereochemistry target values: ML
Details: THE C-TERMINAL 59 RESIDUES ARE NOT VISIBL IN ELECTRON DENSITY, MOST LIKELY THE C-TERMINAL TAIL HAS DEGRADED DURING CRYSTALLIZATION.
RfactorNum. reflection% reflection
Rfree0.2608 1525 5 %
Rwork0.2059 --
obs0.2087 30476 97.15 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.947 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.435 Å20 Å20 Å2
2--9.5266 Å20 Å2
3----5.0916 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 17 413 5282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065049
X-RAY DIFFRACTIONf_angle_d0.926824
X-RAY DIFFRACTIONf_dihedral_angle_d15.8381914
X-RAY DIFFRACTIONf_chiral_restr0.066766
X-RAY DIFFRACTIONf_plane_restr0.003882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37420.37571380.25572614X-RAY DIFFRACTION98
2.3742-2.45910.35781390.24772638X-RAY DIFFRACTION99
2.4591-2.55750.32161380.23012629X-RAY DIFFRACTION99
2.5575-2.67390.29111390.23122636X-RAY DIFFRACTION99
2.6739-2.81480.29771400.22062665X-RAY DIFFRACTION99
2.8148-2.99110.27641400.21922666X-RAY DIFFRACTION99
2.9911-3.2220.26531410.21052684X-RAY DIFFRACTION99
3.222-3.54610.27831410.21512672X-RAY DIFFRACTION99
3.5461-4.05880.22681130.19812151X-RAY DIFFRACTION79
4.0588-5.11210.18821450.15392745X-RAY DIFFRACTION99
5.1121-40.8280.22471510.19432851X-RAY DIFFRACTION99
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)
10.3061-0.1824-0.04670.1776-0.04340.1591-0.06870.0912-0.1101-0.0253-0.035-0.14310.08610.1220.05050.1890.0128-0.00710.14550.01580.238718.3463-16.878629.9754
20.042-0.0275-0.00370.0294-0.00930.0070.04810.00610.0483-0.02050.04150.06420.039-0.0309-0.01440.2460.0055-0.03840.15030.03360.140413.2018-7.59519.8874
30.14290.0086-0.02570.0642-0.07010.17130.0209-0.01160.03170.01530.03490.0377-0.0023-0.00810.08050.0693-0.01080.00290.07510.00120.068811.9479-1.259238.0696
40.17310.0462-0.00440.0320.03760.06-0.0038-0.03110.0926-0.0132-0.02180.0495-0.0103-0.02190.00090.076-0.01910.01550.0463-0.0050.0249-2.581410.746241.5858
50.3390.03470.12770.0778-0.1090.27520.0781-0.1085-0.0242-0.05090.0683-0.0560.0273-0.1218-0.03180.16130.0062-0.01160.1089-0.03610.1734-17.5768-16.778212.3625
60.19460.0051-0.15790.0719-0.00480.12660.1431-0.06250.01580.10260.05320.04390.0187-0.0281-0.06020.2117-0.0136-0.02210.11820.00250.166-17.0747-6.679816.5394
70.15680.028-0.08940.11930.07790.25770.11680.1005-0.04720.02370.0853-0.142-0.14010.04550.17130.03850.0218-0.0161-0.08180.08170.02-11.2285-3.72040.4194
80.1730.03860.06540.0767-0.0510.09810.0326-0.0767-0.04430.04580.0309-0.0564-0.07980.03460.01730.11570.0159-0.00970.1291-0.03440.0826-9.16362.42485.7213
90.1621-0.0013-0.05710.12520.06810.78030.0322-0.04150.07140.1179-0.0410.067-0.14720.2791-0.03390.1203-0.01380.03910.09920.0110.08874.946110.64494.7853
100.0197-0.02210.00490.06110.01140.11080.04320.02330.05950.02150.06830.0244-0.052-0.04350.04640.1566-0.05220.03990.03520.0310.1063-0.133417.8209-1.9739
110.0004-0.00070.00140.01950.02620.03910.03230.079-0.001-0.0091-0.00530.0260.00990.0193-0.01260.0918-0.0067-0.03850.1460.03310.1092-7.058414.3826-11.248
120.04480.01050.04460.1418-0.06550.090.07860.0481-0.03920.0068-0.0643-0.0762-0.09320.0222-0.04220.1297-0.0020.05590.2869-0.04790.09996.54153.3906-12.2216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 3:37
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 38:57)
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 58:174
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 184:245
10X-RAY DIFFRACTION10CHAIN B AND RESSEQ 246:265
11X-RAY DIFFRACTION11CHAIN B AND RESSEQ 266:279
12X-RAY DIFFRACTION12CHAIN B AND RESSEQ 280:301

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