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- PDB-8x88: The Crystal Structure of TNIK from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8x88
TitleThe Crystal Structure of TNIK from Biortus.
ComponentsTRAF2 and NCK-interacting protein kinase
KeywordsTRANSFERASE / Serine/threonine-protein kinase
Function / homology
Function and homology information


microvillus assembly / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / : / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome ...microvillus assembly / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / : / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome / Wnt signaling pathway / MAPK cascade / presynapse / actin cytoskeleton organization / Oxidative Stress Induced Senescence / protein autophosphorylation / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / apical plasma membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / 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. ...Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / 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
TRAF2 and NCK-interacting protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of TNIK from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.
History
DepositionNov 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAF2 and NCK-interacting protein kinase
B: TRAF2 and NCK-interacting protein kinase


Theoretical massNumber of molelcules
Total (without water)69,6082
Polymers69,6082
Non-polymers00
Water77543
1
A: TRAF2 and NCK-interacting protein kinase


Theoretical massNumber of molelcules
Total (without water)34,8041
Polymers34,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRAF2 and NCK-interacting protein kinase


Theoretical massNumber of molelcules
Total (without water)34,8041
Polymers34,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-19 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.750, 112.750, 125.356
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein TRAF2 and NCK-interacting protein kinase


Mass: 34804.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNIK, KIAA0551 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UKE5, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4M Sodium malonate dibasic monohydrate,7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18071 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18071 Å / Relative weight: 1
ReflectionResolution: 2.7→48.82 Å / Num. obs: 25806 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 28.8
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 1.106 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3387

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.535 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.828 / SU ML: 0.237 / Cross valid method: FREE R-VALUE / ESU R: 0.501 / ESU R Free: 0.309
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2561 1226 4.756 %
Rwork0.1981 24551 -
all0.201 --
obs-25777 99.961 %
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: 80.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.406 Å2-0.203 Å2-0 Å2
2---0.406 Å20 Å2
3---1.318 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 0 43 4742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124801
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164485
X-RAY DIFFRACTIONr_angle_refined_deg0.9841.6566476
X-RAY DIFFRACTIONr_angle_other_deg0.3471.57410486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8055581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.083534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9210893
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.15910224
X-RAY DIFFRACTIONr_chiral_restr0.0470.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02912
X-RAY DIFFRACTIONr_nbd_refined0.2220.21144
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24442
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22404
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22468
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2146
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.130.218
X-RAY DIFFRACTIONr_nbd_other0.1410.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0660.26
X-RAY DIFFRACTIONr_mcbond_it4.8558.0382336
X-RAY DIFFRACTIONr_mcbond_other4.8558.0382336
X-RAY DIFFRACTIONr_mcangle_it7.4612.052913
X-RAY DIFFRACTIONr_mcangle_other7.46112.0522914
X-RAY DIFFRACTIONr_scbond_it4.9598.5612465
X-RAY DIFFRACTIONr_scbond_other4.9588.5632466
X-RAY DIFFRACTIONr_scangle_it7.79512.6123563
X-RAY DIFFRACTIONr_scangle_other7.79412.6133564
X-RAY DIFFRACTIONr_lrange_it13.659152.90920123
X-RAY DIFFRACTIONr_lrange_other13.658152.92420118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.7-2.770.357790.33317920.33418710.9270.9311000.333
2.77-2.8460.3571000.32417210.32618210.9050.9381000.324
2.846-2.9280.393780.28817050.29317830.9060.9491000.288
2.928-3.0170.2531010.23416330.23517340.9530.9661000.234
3.017-3.1160.298620.22916170.23116790.9320.9661000.229
3.116-3.2250.289650.22615640.22916290.9460.9651000.226
3.225-3.3460.281710.22914710.23215420.9510.9661000.229
3.346-3.4820.29620.22114650.22315270.9520.971000.221
3.482-3.6360.303640.20314030.20714670.9430.9751000.203
3.636-3.8120.212670.18313200.18513870.9720.981000.183
3.812-4.0160.201620.17512720.17613340.9750.9821000.175
4.016-4.2580.218480.16511940.16712420.970.9831000.165
4.258-4.5490.192740.16411190.16611930.9750.9831000.164
4.549-4.910.236470.15310660.15611130.9680.9841000.153
4.91-5.3720.196560.1799750.1810310.9750.981000.179
5.372-5.9960.293760.1958690.2029450.9510.9771000.195
5.996-6.9030.279340.2237870.2258210.9620.971000.223
6.903-8.4060.286420.1956830.27250.9440.9751000.195
8.406-11.6910.242160.1565550.1585710.9760.9861000.156
11.691-45.5350.349220.2763400.283640.930.95199.45050.276

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