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- PDB-8xpz: The Crystal Structure of TTBK1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xpz
TitleThe Crystal Structure of TTBK1 from Biortus.
ComponentsTau-tubulin kinase 1
KeywordsTRANSFERASE / Kinase / Serine/threonine-protein kinase / ATP-binding
Function / homology
Function and homology information


positive regulation of astrocyte activation / positive regulation of microglial cell activation / microtubule associated complex / tau-protein kinase activity / positive regulation of protein polymerization / substantia nigra development / peptidyl-threonine phosphorylation / peptidyl-tyrosine phosphorylation / tau protein binding / peptidyl-serine phosphorylation ...positive regulation of astrocyte activation / positive regulation of microglial cell activation / microtubule associated complex / tau-protein kinase activity / positive regulation of protein polymerization / substantia nigra development / peptidyl-threonine phosphorylation / peptidyl-tyrosine phosphorylation / tau protein binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / learning or memory / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / positive regulation of gene expression / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tau-tubulin kinase 1, catalytic domain / : / 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
Tau-tubulin kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Ni, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of TTBK1 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Ni, C.
History
DepositionJan 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tau-tubulin kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0083
Polymers37,8841
Non-polymers1242
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.905, 40.204, 49.533
Angle α, β, γ (deg.)90.000, 103.725, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

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Components

#1: Protein Tau-tubulin kinase 1 / Brain-derived tau kinase


Mass: 37883.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTBK1, BDTK, KIAA1855 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5TCY1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5M LiCl, 0.1M Tris-HCl pH8.5, 28% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95355 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95355 Å / Relative weight: 1
ReflectionResolution: 2.6→48.165 Å / Num. obs: 10211 / % possible obs: 99 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.4
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.907 / Num. unique obs: 1215

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.165 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.404 / SU ML: 0.358 / Cross valid method: FREE R-VALUE / ESU R Free: 0.363
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2733 476 4.662 %
Rwork0.2009 9734 -
all0.205 --
obs-10210 98.838 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 58.329 Å2
Baniso -1Baniso -2Baniso -3
1-3.551 Å2-0 Å2-1.409 Å2
2--3.566 Å20 Å2
3----5.744 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 8 39 2436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132447
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172375
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.6473283
X-RAY DIFFRACTIONr_angle_other_deg1.151.5875453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9145292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41721.056142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06615459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9141522
X-RAY DIFFRACTIONr_chiral_restr0.0570.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
X-RAY DIFFRACTIONr_nbd_refined0.1870.2449
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.22146
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21137
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0740.28
X-RAY DIFFRACTIONr_nbd_other0.1520.243
X-RAY DIFFRACTIONr_mcbond_it4.0715.9561171
X-RAY DIFFRACTIONr_mcbond_other4.0675.9531170
X-RAY DIFFRACTIONr_mcangle_it6.3448.9381462
X-RAY DIFFRACTIONr_mcangle_other6.3428.9421463
X-RAY DIFFRACTIONr_scbond_it3.6566.3491276
X-RAY DIFFRACTIONr_scbond_other3.6556.3491277
X-RAY DIFFRACTIONr_scangle_it6.0779.321821
X-RAY DIFFRACTIONr_scangle_other6.0769.321822
X-RAY DIFFRACTIONr_lrange_it11.587111.1539868
X-RAY DIFFRACTIONr_lrange_other11.588111.1519867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6680.388430.371722X-RAY DIFFRACTION98.9651
2.668-2.7410.333330.323681X-RAY DIFFRACTION98.892
2.741-2.820.361330.309675X-RAY DIFFRACTION99.859
2.82-2.9070.484260.265671X-RAY DIFFRACTION98.0309
2.907-3.0020.253240.231625X-RAY DIFFRACTION99.8462
3.002-3.1070.357250.222633X-RAY DIFFRACTION98.7988
3.107-3.2240.261260.225586X-RAY DIFFRACTION99.6743
3.224-3.3560.354270.219607X-RAY DIFFRACTION98.908
3.356-3.5050.278270.219536X-RAY DIFFRACTION99.8227
3.505-3.6750.284380.187516X-RAY DIFFRACTION98.7522
3.675-3.8740.263300.18489X-RAY DIFFRACTION99.8077
3.874-4.1080.28210.155494X-RAY DIFFRACTION99.0385
4.108-4.3910.149200.142439X-RAY DIFFRACTION98.4979
4.391-4.7420.261360.136399X-RAY DIFFRACTION99.0888
4.742-5.1920.192220.179374X-RAY DIFFRACTION95.1923
5.192-5.8030.367100.206355X-RAY DIFFRACTION96.817
5.803-6.6950.268110.23321X-RAY DIFFRACTION99.6997
6.695-8.1860.27580.197278X-RAY DIFFRACTION98.6207
8.186-11.5210.17570.157205X-RAY DIFFRACTION98.6047
11.521-48.1650.27890.222128X-RAY DIFFRACTION95.8042

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