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- PDB-5o0y: TLK2 kinase domain from human -

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Basic information

Entry
Database: PDB / ID: 5o0y
TitleTLK2 kinase domain from human
ComponentsSerine/threonine-protein kinase tousled-like 2
KeywordsTRANSFERASE / Kinase / ATPgS / chromatin remodelling / DNA replication
Function / homology
Function and homology information


regulation of chromatin organization / intermediate filament / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / localization / negative regulation of autophagy / chromosome segregation / cellular response to gamma radiation / chromatin organization / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase ...regulation of chromatin organization / intermediate filament / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / localization / negative regulation of autophagy / chromosome segregation / cellular response to gamma radiation / chromatin organization / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / perinuclear region of cytoplasm / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
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
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase tousled-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsMortuza, G.B. / Montoya, G.
CitationJournal: Nat Commun / Year: 2018
Title: Molecular basis of Tousled-Like Kinase 2 activation.
Authors: Mortuza, G.B. / Hermida, D. / Pedersen, A.K. / Segura-Bayona, S. / Lopez-Mendez, B. / Redondo, P. / Ruther, P. / Pozdnyakova, I. / Garrote, A.M. / Munoz, I.G. / Villamor-Paya, M. / Jauset, C. ...Authors: Mortuza, G.B. / Hermida, D. / Pedersen, A.K. / Segura-Bayona, S. / Lopez-Mendez, B. / Redondo, P. / Ruther, P. / Pozdnyakova, I. / Garrote, A.M. / Munoz, I.G. / Villamor-Paya, M. / Jauset, C. / Olsen, J.V. / Stracker, T.H. / Montoya, G.
History
DepositionMay 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase tousled-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9162
Polymers67,3931
Non-polymers5231
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint1 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.020, 126.020, 126.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Serine/threonine-protein kinase tousled-like 2 / HsHPK / PKU-alpha / Tousled-like kinase 2


Mass: 67392.508 Da / Num. of mol.: 1 / Fragment: UNP residues 191-755
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86UE8, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20 mM HEPES pH 7, 2M Li2SO4, 10mM MgCl2 1M Na/K tartrate, 0.1M Tris pH7, 200mM LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.85→72.76 Å / Num. obs: 15761 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 13.07
Reflection shellResolution: 2.857→2.959 Å / Num. unique obs: 15761 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→89.11 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 35.731 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20979 794 5 %RANDOM
Rwork0.18251 ---
obs0.18392 14971 99.94 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.882 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.86→89.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 31 0 2390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192451
X-RAY DIFFRACTIONr_bond_other_d0.0010.022244
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.9813324
X-RAY DIFFRACTIONr_angle_other_deg0.91835229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4335287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66224.37119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1815432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3751513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0338.7441151
X-RAY DIFFRACTIONr_mcbond_other1.0318.7451150
X-RAY DIFFRACTIONr_mcangle_it1.84813.1181437
X-RAY DIFFRACTIONr_mcangle_other1.84813.1181438
X-RAY DIFFRACTIONr_scbond_it0.9948.9721300
X-RAY DIFFRACTIONr_scbond_other0.9938.9731301
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.80313.421888
X-RAY DIFFRACTIONr_long_range_B_refined4.4259591
X-RAY DIFFRACTIONr_long_range_B_other4.4259592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.856→2.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 58 -
Rwork0.373 1114 -
obs--99.24 %
Refinement TLS params.Method: refined / Origin x: -13.399 Å / Origin y: -25.527 Å / Origin z: 11.992 Å
111213212223313233
T0.0788 Å20.0162 Å2-0.0114 Å2-0.125 Å20.0125 Å2--0.1827 Å2
L0.4189 °20.0585 °2-0.8597 °2-0.5892 °2-0.6728 °2--2.3735 °2
S-0.0154 Å °-0.0881 Å °0.0338 Å °-0.0815 Å °0.0225 Å °-0.1162 Å °0.0971 Å °0.0572 Å °-0.0071 Å °

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