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- PDB-8wgf: The Crystal Structure of JNK3 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8wgf
TitleThe Crystal Structure of JNK3 from Biortus.
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / Kinase / Serine/threonine-protein kinase / Biological rhythms / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm ...JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm / cellular senescence / rhythmic process / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Wang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of JNK3 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Wang, J.
History
DepositionSep 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5903
Polymers42,0601
Non-polymers5312
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-12 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.956, 71.003, 106.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase 10


Mass: 42059.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10 / Production host: Escherichia coli (E. coli) / References: UniProt: P53779
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 16% PEG MME (average Mr=550), 10% ethylene glycol, 20mM beta-mercaptoethanol, 100mM HEPES (pH7.3)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1806 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1806 Å / Relative weight: 1
ReflectionResolution: 1.85→46 Å / Num. obs: 33935 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 25.7
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.776 / Num. unique obs: 2097

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→38.638 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.799 / SU ML: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.154
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2663 1645 4.861 %
Rwork0.2096 32198 -
all0.212 --
obs-33843 99.847 %
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: 43.429 Å2
Baniso -1Baniso -2Baniso -3
1-5.522 Å20 Å2-0 Å2
2---2.454 Å2-0 Å2
3----3.068 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 32 208 3042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132916
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172788
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.6493949
X-RAY DIFFRACTIONr_angle_other_deg1.2621.5816431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6035346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81222.745153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36915526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4151517
X-RAY DIFFRACTIONr_chiral_restr0.0740.2373
X-RAY DIFFRACTIONr_chiral_restr_other0.1230.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02652
X-RAY DIFFRACTIONr_nbd_refined0.2120.2684
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22761
X-RAY DIFFRACTIONr_nbtor_refined0.170.21385
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21376
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2191
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1110.28
X-RAY DIFFRACTIONr_nbd_other0.2260.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.27
X-RAY DIFFRACTIONr_mcbond_it3.7344.3621381
X-RAY DIFFRACTIONr_mcbond_other3.7354.3591380
X-RAY DIFFRACTIONr_mcangle_it5.3966.5151722
X-RAY DIFFRACTIONr_mcangle_other5.3956.5181723
X-RAY DIFFRACTIONr_scbond_it4.2644.7371535
X-RAY DIFFRACTIONr_scbond_other4.2644.7371535
X-RAY DIFFRACTIONr_scangle_it6.1686.9492225
X-RAY DIFFRACTIONr_scangle_other6.1676.9482226
X-RAY DIFFRACTIONr_lrange_it9.06451.4763387
X-RAY DIFFRACTIONr_lrange_other9.07651.2543353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.3571150.3492344X-RAY DIFFRACTION99.8782
1.898-1.950.3881240.3832288X-RAY DIFFRACTION99.9586
1.95-2.0060.3441260.3022213X-RAY DIFFRACTION100
2.006-2.0680.278980.2642171X-RAY DIFFRACTION99.9559
2.068-2.1360.2511110.2512103X-RAY DIFFRACTION99.9097
2.136-2.2110.367950.2522022X-RAY DIFFRACTION99.5299
2.211-2.2940.327870.2851956X-RAY DIFFRACTION98.8389
2.294-2.3880.377950.2221896X-RAY DIFFRACTION100
2.388-2.4940.294940.221814X-RAY DIFFRACTION100
2.494-2.6150.333830.2181745X-RAY DIFFRACTION100
2.615-2.7560.341880.2281659X-RAY DIFFRACTION100
2.756-2.9230.297770.2031585X-RAY DIFFRACTION100
2.923-3.1240.244830.2031493X-RAY DIFFRACTION99.9366
3.124-3.3740.275680.2161399X-RAY DIFFRACTION100
3.374-3.6950.23680.1951278X-RAY DIFFRACTION99.9258
3.695-4.1290.25640.1771158X-RAY DIFFRACTION99.9182
4.129-4.7640.21510.1541053X-RAY DIFFRACTION100
4.764-5.8250.203560.161882X-RAY DIFFRACTION100
5.825-8.1980.216380.194713X-RAY DIFFRACTION100
8.198-38.6380.218240.168426X-RAY DIFFRACTION98.4683

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