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

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Basic information

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


positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / anoikis / positive regulation of neutrophil chemotaxis / cytoplasmic vesicle / calmodulin binding / protein phosphorylation / non-specific serine/threonine protein kinase ...positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / anoikis / positive regulation of neutrophil chemotaxis / cytoplasmic vesicle / calmodulin binding / protein phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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. ...Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ADENOSINE MONOPHOSPHATE / Death-associated protein kinase 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1Jan 15, 2014Group: Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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)84,80710
Polymers83,5922
Non-polymers1,2158
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-66.2 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.140, 85.370, 123.990
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-RELATED PROTEIN 1 / DAP KINASE 2 / DRP-1


Mass: 41795.848 Da / Num. of mol.: 2 / Fragment: RESIDUES 13-311
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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.: 686 / 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 Å3/Da / Density % sol: 38.46 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 53144 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 20.31 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5

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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: 1.9→42.685 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 21.76 / 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
Rfree0.2148 2658 5 %
Rwork0.1718 --
obs0.1739 53125 99.24 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.327 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.1984 Å20 Å20 Å2
2--4.0243 Å20 Å2
3----5.2227 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 72 686 5610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065174
X-RAY DIFFRACTIONf_angle_d1.0237017
X-RAY DIFFRACTIONf_dihedral_angle_d15.6181967
X-RAY DIFFRACTIONf_chiral_restr0.061783
X-RAY DIFFRACTIONf_plane_restr0.004902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-1.93480.3041350.252552X-RAY DIFFRACTION97
1.9348-1.9720.26991380.21832623X-RAY DIFFRACTION99
1.972-2.01230.25451370.20042612X-RAY DIFFRACTION99
2.0123-2.0560.23781380.18472625X-RAY DIFFRACTION99
2.056-2.10390.22261390.17662629X-RAY DIFFRACTION100
2.1039-2.15650.21621390.17352638X-RAY DIFFRACTION100
2.1565-2.21480.23671390.15732641X-RAY DIFFRACTION99
2.2148-2.27990.2331370.17142617X-RAY DIFFRACTION99
2.2799-2.35350.2261390.16062633X-RAY DIFFRACTION100
2.3535-2.43760.25181400.16932664X-RAY DIFFRACTION100
2.4376-2.53520.21851400.17072653X-RAY DIFFRACTION99
2.5352-2.65060.23471390.17062644X-RAY DIFFRACTION99
2.6506-2.79030.26661390.1632637X-RAY DIFFRACTION99
2.7903-2.96510.20911410.16432687X-RAY DIFFRACTION99
2.9651-3.1940.2411400.17562659X-RAY DIFFRACTION99
3.194-3.51520.2251420.17842696X-RAY DIFFRACTION100
3.5152-4.02360.17521420.14542697X-RAY DIFFRACTION100
4.0236-5.0680.14381440.1442730X-RAY DIFFRACTION99
5.068-42.69580.20231500.20072830X-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)
10.11250.2165-0.08430.6673-0.27630.2098-0.28830.0986-0.1369-0.40960.04010.08870.2959-0.0582-0.02320.23310.1234-0.00310.1364-0.02170.1871-13.5106-15.6216-32.0117
20.54810.0216-0.39490.15570.4041.5080.36330.15290.0776-0.5480.19880.1961-0.05560.18830.08110.31650.0695-0.08610.15390.04640.2254-15.0793-1.4935-41.2925
30.5818-0.46160.06350.5251-0.11350.36050.0325-0.0188-0.0752-0.0469-0.00590.05050.06230.0302-0.01460.0979-0.0032-0.01560.0938-0.00390.1052-20.5794-1.1363-22.3977
40.6357-0.0883-0.09030.1669-0.12910.59710.0153-0.04170.0011-0.03790.02430.0337-0.0743-0.1038-0.0160.0919-0.00310.00090.09070.00490.0844-34.208110.873-20.4146
50.5969-0.0684-0.0050.3329-0.2610.51850.048-0.0385-0.12120.0908-0.0368-0.02-0.0837-0.05130.00590.1619-0.0291-0.03090.15890.0130.1574-49.4965-16.4862-50.8181
60.93720.0006-0.07770.2584-0.01940.82010.1062-0.08570.13940.28230.0074-0.0322-0.0883-0.2193-0.00350.2307-0.0244-0.03860.1595-0.02790.1577-47.6242-1.845-41.3291
70.54190.49620.23680.6480.27020.17050.00850.1214-0.11340.06980.0395-0.16160.0212-0.0112-0.01580.11570.035-0.01240.12130.00640.1398-42.593-3.6169-61.476
80.46680.0971-0.01010.24340.0050.5330.17950.0558-0.0662-0.0849-0.0706-0.0226-0.12550.036-0.02860.11930.0183-0.01720.1362-0.01960.1141-40.2548-2.4687-60.873
90.8050.0042-0.30810.42860.29310.98140.05980.05750.1047-0.0385-0.0179-0.0411-0.12040.0959-0.03380.13020.01150.02680.12240.00970.1048-31.567512.5005-58.6982
100.04130.05970.01030.14870.05340.03240.02160.4738-0.0658-0.05390.03840.0499-0.1804-0.1520.11690.01930.09290.21290.3358-0.06260.2406-24.87892.7339-73.6507
110.0555-0.01920.02510.06230.00180.1517-0.0404-0.10410.0074-0.03630.01720.04080.0087-0.0189-0.03750.15290.0394-0.12160.2195-0.14970.196-22.4401-8.3704-28.6738
120.07310.03550.06170.05460.04820.0893-0.06850.0374-0.06360.0323-0.0328-0.0518-0.0067-0.046-0.00430.13880.0163-0.06410.20070.04820.16-40.0624-9.625-54.8436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:45)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 46:70)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 71:174)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 175:301)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 3:45)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 46:70)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 71:133)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 134:164)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 165:279)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 280:301)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 1302:1302)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 1302:1302)

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