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- PDB-1wmk: Human death-associated kinase DRP-1, mutant S308D d40 -

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Basic information

Entry
Database: PDB / ID: 1wmk
TitleHuman death-associated kinase DRP-1, mutant S308D d40
ComponentsDeath-associated protein kinase 2
KeywordsTRANSFERASE / protein kinase / autoinhibitory helix
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 / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Single helix bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 ...Single helix bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / 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: 3.6 Å
AuthorsKursula, P. / Shani, G. / Kimchi, A. / Wilmanns, M.
CitationJournal: To be Published
Title: Structure of the inhibited conformation of DRP-1 kinase
Authors: Kursula, P. / Shani, G. / Kimchi, A. / Wilmanns, M.
History
DepositionJul 11, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 1.4Oct 25, 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
E: Death-associated protein kinase 2
C: Death-associated protein kinase 2
B: Death-associated protein kinase 2
F: Death-associated protein kinase 2
D: Death-associated protein kinase 2
H: Death-associated protein kinase 2
G: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)297,3488
Polymers297,3488
Non-polymers00
Water0
1
A: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,1681
Polymers37,1681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,1681
Polymers37,1681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,1681
Polymers37,1681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,1681
Polymers37,1681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,1681
Polymers37,1681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,1681
Polymers37,1681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
H: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,1681
Polymers37,1681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
G: Death-associated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)37,1681
Polymers37,1681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.190, 143.290, 255.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
31C
41B
51F
61D
71H
81G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 1

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ARGARGAA2 - 3043 - 305
2LEULEUEB2 - 3143 - 315
3ARGARGCC2 - 3043 - 305
4CYSCYSBD2 - 3153 - 316
5ARGARGFE2 - 3043 - 305
6CYSCYSDF2 - 3153 - 316
7TRPTRPHG2 - 3053 - 306
8LEULEUGH2 - 3143 - 315

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Components

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


Mass: 37168.492 Da / Num. of mol.: 8 / Fragment: residues 1-320 / Mutation: S308D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG, sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.6→20 Å / Num. all: 37261 / Num. obs: 37261 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 63 Å2 / Rsym value: 0.173 / Net I/σ(I): 7.6
Reflection shellResolution: 3.6→3.7 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2894 / Rsym value: 0.434 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SXO

1sxo
PDB Unreleased entry


Resolution: 3.6→20 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.873 / SU B: 53.183 / SU ML: 0.732
Isotropic thermal model: GROUP B FACTOR REFINEMENT IN CNS, OVERALL B FACTOR REFINEMENT IN REFMAC5
Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.814 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GROUP B FACTOR REFINEMENT IN CNS, OVERALL B FACTOR REFINEMENT IN REFMAC5
RfactorNum. reflection% reflectionSelection details
Rfree0.29577 1864 5 %RANDOM
Rwork0.27633 ---
all0.2773 37254 --
obs0.2773 37254 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 130.433 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--4.76 Å20 Å2
3----4.17 Å2
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19951 0 0 0 19951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02120335
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218716
X-RAY DIFFRACTIONr_angle_refined_deg0.8741.95727437
X-RAY DIFFRACTIONr_angle_other_deg0.7343536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.74252459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.43624.3311016
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.596153760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.40815144
X-RAY DIFFRACTIONr_chiral_restr0.0520.23075
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0222445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024139
X-RAY DIFFRACTIONr_nbd_refined0.1760.23506
X-RAY DIFFRACTIONr_nbd_other0.20.219956
X-RAY DIFFRACTIONr_nbtor_other0.0820.212281
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2177
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.24
Refine LS restraints NCS

Ens-ID: 1 / Number: 4786 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.1

Dom-IDAuth asym-IDRms dev position (Å)
1A0.04
2E0.04
3C0.04
4B0.04
5F0.03
6D0.04
7H0.04
8G0.03
LS refinement shellResolution: 3.6→3.691 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.467 185
Rwork0.46 2427

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