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- PDB-1zws: Crystal structure of the catalytic domain of human DRP-1 kinase -

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Basic information

Entry
Database: PDB / ID: 1zws
TitleCrystal structure of the catalytic domain of human DRP-1 kinase
ComponentsDAP-kinase related protein 1
KeywordsTRANSFERASE / protein kinase / twinning
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
Death-associated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKursula, P. / Schunck, H. / Wilmanns, M.
CitationJournal: To be Published
Title: Crystal structure of the catalytic domain of human DRP-1 kinase
Authors: Kursula, P. / Schunck, H. / Wilmanns, M.
History
DepositionJun 6, 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: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DAP-kinase related protein 1
B: DAP-kinase related protein 1
C: DAP-kinase related protein 1
D: DAP-kinase related protein 1
E: DAP-kinase related protein 1
F: DAP-kinase related protein 1
G: DAP-kinase related protein 1
H: DAP-kinase related protein 1


Theoretical massNumber of molelcules
Total (without water)264,7748
Polymers264,7748
Non-polymers00
Water00
1
A: DAP-kinase related protein 1
B: DAP-kinase related protein 1


Theoretical massNumber of molelcules
Total (without water)66,1942
Polymers66,1942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DAP-kinase related protein 1
D: DAP-kinase related protein 1


Theoretical massNumber of molelcules
Total (without water)66,1942
Polymers66,1942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DAP-kinase related protein 1
F: DAP-kinase related protein 1


Theoretical massNumber of molelcules
Total (without water)66,1942
Polymers66,1942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: DAP-kinase related protein 1
H: DAP-kinase related protein 1


Theoretical massNumber of molelcules
Total (without water)66,1942
Polymers66,1942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.620, 211.830, 128.420
Angle α, β, γ (deg.)90.00, 101.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DAP-kinase related protein 1


Mass: 33096.770 Da / Num. of mol.: 8 / Fragment: catalytic domain
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

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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: 2.7 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris, PEG, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.095 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.095 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 55013 / Num. obs: 55013 / % possible obs: 90.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 48 Å2 / Rsym value: 0.115 / Net I/σ(I): 6.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 4903 / Rsym value: 0.503 / % possible all: 84.2

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
MOLREPphasing
CNS1.1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sxo

1sxo
PDB Unreleased entry


Resolution: 2.9→20 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber
Details: The crystal form is perfectly twinned with the operator -h,-k,h+l, twinning fraction = 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 937 -The test reflections were randomly selected, based on the twinning operator
Rwork0.2204 ---
all-55013 --
obs-55013 90.8 %-
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18024 0 0 0 18024
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.78

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