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- PDB-1z9x: Human DRP-1 kinase, W305S S308A D40 mutant, crystal form with 3 m... -

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Basic information

Entry
Database: PDB / ID: 1z9x
TitleHuman DRP-1 kinase, W305S S308A D40 mutant, crystal form with 3 monomers in the asymmetric unit
ComponentsDeath-associated protein kinase 2
KeywordsTRANSFERASE / protein kinase / autoinhibitory helix / dimerization
Function / homology
Function and homology information


autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / positive regulation of eosinophil chemotaxis / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of neutrophil chemotaxis / anoikis / regulation of autophagy / cytoplasmic vesicle / regulation of apoptotic process / protein autophosphorylation ...autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / positive regulation of eosinophil chemotaxis / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of neutrophil chemotaxis / anoikis / regulation of autophagy / cytoplasmic vesicle / regulation of apoptotic process / protein autophosphorylation / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / ATP binding / identical protein 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
Death-associated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.93 Å
AuthorsKursula, P. / Lehmann, F. / Shani, G. / Kimchi, A. / Wilmanns, M.
CitationJournal: To be Published
Title: A structural insight into the double-locking mechanism of the human death-associated DRP-1 kinase
Authors: Kursula, P. / Lehmann, F. / Shani, G. / Kimchi, A. / Wilmanns, M.
History
DepositionApr 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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
C: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)111,1543
Polymers111,1543
Non-polymers00
Water00
1
A: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,0511
Polymers37,0511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,0511
Polymers37,0511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,0511
Polymers37,0511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.400, 62.990, 150.970
Angle α, β, γ (deg.)90.00, 110.98, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA2 - 953 - 96
21GLUGLULEULEUBB2 - 953 - 96
31GLUGLULEULEUCC2 - 953 - 96
12VALVALARGARGAA96 - 30497 - 305
22VALVALARGARGBB96 - 30497 - 305
32VALVALARGARGCC96 - 30497 - 305

NCS ensembles :
ID
1
2

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Components

#1: Protein Death-associated protein kinase 2 / DAP kinase 2 / DAP- kinase related protein 1 / DRP-1


Mass: 37051.371 Da / Num. of mol.: 3 / Fragment: Residues 1-320 / Mutation: S308A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK2 / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / Keywords: D40 / References: UniProt: Q9UIK4, EC: 2.7.1.37

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 14 % PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8 / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 3.93→20 Å / Num. all: 9532 / Num. obs: 9532 / % possible obs: 94.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 89 Å2 / Rsym value: 0.052 / Net I/σ(I): 15.4
Reflection shellResolution: 3.93→4 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 380 / Rsym value: 0.176 / % possible all: 79.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1SXO

1sxo
PDB Unreleased entry


Resolution: 3.93→20 Å / Cor.coef. Fo:Fc: 0.8 / Cor.coef. Fo:Fc free: 0.755 / SU B: 243.388 / SU ML: 1.535 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 1.297 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35074 474 5 %RANDOM
Rwork0.32849 ---
all0.32956 9470 --
obs0.32956 9470 94.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 103.465 Å2
Baniso -1Baniso -2Baniso -3
1--11.66 Å20 Å2-2.17 Å2
2--13.24 Å20 Å2
3----3.13 Å2
Refinement stepCycle: LAST / Resolution: 3.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7407 0 0 0 7407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227554
X-RAY DIFFRACTIONr_angle_refined_deg0.8921.96310191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2985906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5224.252381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.855151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4671554
X-RAY DIFFRACTIONr_chiral_restr0.0520.21137
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025682
X-RAY DIFFRACTIONr_nbd_refined0.1740.23100
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6250.2242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4740.219
X-RAY DIFFRACTIONr_mcbond_it0.0211.54703
X-RAY DIFFRACTIONr_mcangle_it0.03427359
X-RAY DIFFRACTIONr_scbond_it0.05233192
X-RAY DIFFRACTIONr_scangle_it0.0824.52832
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A775tight positional0.020.05
12B775tight positional0.020.05
13C775tight positional0.040.05
21A1695tight positional0.020.05
22B1695tight positional0.020.05
23C1695tight positional0.030.05
11A775tight thermal0.010.5
12B775tight thermal0.010.5
13C775tight thermal0.010.5
21A1695tight thermal0.010.5
22B1695tight thermal0.010.5
23C1695tight thermal0.010.5
LS refinement shellResolution: 3.93→4.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 30 -
Rwork0.356 570 -
obs--86.96 %
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)
17.3239-0.44290.33737.4425-1.87315.57250.10550.1790.48850.7170.07520.2012-0.36370.7328-0.1807-0.5650.1924-0.0496-0.2802-0.0717-0.94270.7219-0.064723.4979
24.92040.09291.36796.5763-1.33458.15120.04490.27910.21940.9940.11460.27410.1037-0.5939-0.1595-0.60440.13030.0761-0.05140.0348-0.477395.30248.150623.2078
34.22210.4113-0.4137.2298-0.85099.70790.2579-0.5317-0.65020.2955-0.4697-0.24330.83910.0430.2118-0.58780.24840.0847-1.2867-0.0906-0.463883.18626.96165.6757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 3043 - 305
2X-RAY DIFFRACTION2BB2 - 3043 - 305
3X-RAY DIFFRACTION3CC2 - 3043 - 305

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