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- PDB-2a27: Human DRP-1 kinase, W305S S308A D40 mutant, crystal form with 8 m... -

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Basic information

Entry
Database: PDB / ID: 2a27
TitleHuman DRP-1 kinase, W305S S308A D40 mutant, crystal form with 8 monomers in the asymmetric unit
ComponentsDeath-associated protein kinase 2
KeywordsTRANSFERASE / protein kinase / autoinhibition
Function / homology
Function and homology information


positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of neutrophil chemotaxis / anoikis / protein autophosphorylation / cytoplasmic vesicle / regulation of apoptotic process ...positive regulation of eosinophil chemotaxis / autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / neutrophil migration / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of neutrophil chemotaxis / anoikis / protein autophosphorylation / cytoplasmic vesicle / regulation of apoptotic process / calmodulin binding / protein phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / regulation of autophagy / positive regulation of apoptotic process / 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
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Death-associated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKursula, P. / Lehmann, F. / Shani, G. / Kimchi, A. / Wilmanns, M.
CitationJournal: To be Published
Title: Human DRP-1 kinase, W305S S308A D40 mutant, crystal form with 8 monomers in the asymmetric unit
Authors: Kursula, P. / Lehmann, F. / Shani, G. / Kimchi, A. / Wilmanns, M.
History
DepositionJun 22, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
D: Death-associated protein kinase 2
E: Death-associated protein kinase 2
F: Death-associated protein kinase 2
G: Death-associated protein kinase 2
H: Death-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,43716
Polymers296,2038
Non-polymers1,2348
Water3,171176
1
A: Death-associated protein kinase 2
E: Death-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3594
Polymers74,0512
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Death-associated protein kinase 2
C: Death-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3594
Polymers74,0512
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Death-associated protein kinase 2
G: Death-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3594
Polymers74,0512
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Death-associated protein kinase 2
H: Death-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3594
Polymers74,0512
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.120, 113.350, 247.310
Angle α, β, γ (deg.)90.00, 95.09, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51F
61E
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 4

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERSERAA2 - 3053 - 306
2ARGARGBB2 - 3043 - 305
3ARGARGCC2 - 3043 - 305
4SERSERDD2 - 3053 - 306
5ARGARGFF2 - 3043 - 305
6ARGARGEE2 - 3043 - 305
7ARGARGGG2 - 3043 - 305
8SERSERHH2 - 3053 - 306

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Components

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


Mass: 37025.352 Da / Num. of mol.: 8 / Fragment: D40 truncation / Mutation: W305S, S308A
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
#2: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.8 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8416 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8416 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. all: 87689 / Num. obs: 87689 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 63 Å2 / Rsym value: 0.081 / Net I/σ(I): 11.4
Reflection shellResolution: 3→3.2 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 15360 / 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 / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 38.161 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement / Cross valid method: THROUGHOUT / ESU R: 1.703 / ESU R Free: 0.357 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23844 4395 5 %RANDOM
Rwork0.21744 ---
all0.21852 87443 --
obs0.21852 87443 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.853 Å2
Baniso -1Baniso -2Baniso -3
1-7.37 Å20 Å2-1.68 Å2
2---1.44 Å20 Å2
3----6.23 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19763 0 64 176 20003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02120195
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218647
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.95927227
X-RAY DIFFRACTIONr_angle_other_deg0.72343435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55652419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21324.3031018
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.715153766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.89715146
X-RAY DIFFRACTIONr_chiral_restr0.0670.23051
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0222143
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024107
X-RAY DIFFRACTIONr_nbd_refined0.1970.24165
X-RAY DIFFRACTIONr_nbd_other0.2020.221141
X-RAY DIFFRACTIONr_nbtor_other0.0840.212153
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2230
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3220.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.25
X-RAY DIFFRACTIONr_mcbond_it0.599315864
X-RAY DIFFRACTIONr_mcbond_other0.20134910
X-RAY DIFFRACTIONr_mcangle_it0.787419623
X-RAY DIFFRACTIONr_scbond_it0.70849313
X-RAY DIFFRACTIONr_scangle_it1.09557604
Refine LS restraints NCS

Ens-ID: 1 / Number: 4777 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.150.2
2Bmedium positional0.20.2
3Cmedium positional0.120.2
4Dmedium positional0.130.2
5Fmedium positional0.10.2
6Emedium positional0.140.2
7Gmedium positional0.090.2
8Hmedium positional0.090.2
1Amedium thermal0.663
2Bmedium thermal0.813
3Cmedium thermal0.573
4Dmedium thermal0.453
5Fmedium thermal0.343
6Emedium thermal0.363
7Gmedium thermal0.343
8Hmedium thermal0.333
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 293
Rwork0.356 6051
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)
11.64290.483-0.05774.2192-0.96573.0955-0.0383-0.3940.03380.1589-0.0672-0.1267-0.630.22440.1055-0.5538-0.03460.0271-0.5996-0.0319-0.462438.8999-0.012331.0106
20.97750.4298-0.77254.2145-1.80643.7039-0.04910.145-0.08760.21040.01220.12510.0065-0.21930.037-0.5803-0.0336-0.0373-0.8796-0.0481-0.340234.709314.4793-2.191
35.74230.44311.17231.70680.57962.3432-0.00370.6645-0.4814-0.0877-0.08740.00090.3126-0.10320.091-0.4940.01790.124-0.3932-0.1752-0.324532.32011.8181-35.6949
44.5326-0.6314-0.36181.7165-0.48253.10590.01220.6039-0.0717-0.44110.0974-0.0446-0.110.4479-0.1097-0.3294-0.17030.0612-0.062-0.3689-0.25695.3384-1.504-60.2128
53.4414-0.3303-1.10682.23751.07322.72780.0792-0.55890.31730.0868-0.1328-0.0687-0.63390.47640.0536-0.0683-0.3147-0.18360.2987-0.0237-0.271852.453811.659962.0399
64.0737-0.3688-0.77441.5897-0.45044.0826-0.0498-0.04250.07190.0771-0.04110.0686-0.59620.32760.09090.246-0.1762-0.18090.2352-0.3593-0.093437.76822.214193.8291
71.2750.1224-0.69554.1415-0.18782.1926-0.02720.06510.0809-0.43720.0934-0.0623-0.05190.262-0.06620.3805-0.2269-0.10010.2903-0.1328-0.27641.5955-5.3277-95.8799
82.15340.46130.38923.4990.09291.8688-0.0317-0.03250.01260.1369-0.09180.2584-0.19310.00060.12350.4577-0.0720.0050.2447-0.152-0.355249.038424.5404127.7413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 3053 - 306
2X-RAY DIFFRACTION2BB2 - 3043 - 305
3X-RAY DIFFRACTION3CC2 - 3043 - 305
4X-RAY DIFFRACTION4DD2 - 3053 - 306
5X-RAY DIFFRACTION5EE2 - 3043 - 305
6X-RAY DIFFRACTION6FF2 - 3043 - 305
7X-RAY DIFFRACTION7GG2 - 3043 - 305
8X-RAY DIFFRACTION8HH2 - 3053 - 306

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