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- PDB-8xfm: The Crystal Structure of MNK2 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xfm
TitleThe Crystal Structure of MNK2 from Biortus.
ComponentsMAP kinase-interacting serine/threonine-protein kinase 2
KeywordsTRANSFERASE / Kinase / Serine/threonine-protein kinase / Apoptosis / ATP-binding
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / cellular response to arsenic-containing substance / calmodulin-dependent protein kinase activity / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / PML body / regulation of translation / cell surface receptor signaling pathway / nuclear body / calmodulin binding ...calcium-dependent protein serine/threonine kinase activity / cellular response to arsenic-containing substance / calmodulin-dependent protein kinase activity / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / PML body / regulation of translation / cell surface receptor signaling pathway / nuclear body / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
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
Chem-A1LU6 / MAP kinase-interacting serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of MNK2 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J.
History
DepositionDec 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAP kinase-interacting serine/threonine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9974
Polymers35,5181
Non-polymers4783
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.859, 103.859, 73.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MAP kinase-interacting serine/threonine-protein kinase 2


Mass: 35518.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MKNK2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HBH9
#2: Chemical ChemComp-A1LU6 / 5-(3-azanyl-1~{H}-indazol-6-yl)-1-[(3-chlorophenyl)methyl]pyridin-2-one


Mass: 350.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15ClN4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M NH4Ac, 0.1M Bis-Tris pH5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→45.013 Å / Num. obs: 14349 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 27.5
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 968

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.013 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.097 / SU ML: 0.208 / Cross valid method: FREE R-VALUE / ESU R: 0.362 / ESU R Free: 0.275
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2536 645 4.495 %
Rwork0.1901 13704 -
all0.193 --
obs-14349 99.951 %
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: 62.713 Å2
Baniso -1Baniso -2Baniso -3
1--1.031 Å2-0.516 Å2-0 Å2
2---1.031 Å20 Å2
3---3.346 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 30 76 2305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122291
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162117
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.6683093
X-RAY DIFFRACTIONr_angle_other_deg0.4151.5914875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.631515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90910390
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg4.687104
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.53610116
X-RAY DIFFRACTIONr_chiral_restr0.0560.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02544
X-RAY DIFFRACTIONr_nbd_refined0.2040.2484
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22009
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21125
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21189
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0690.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.222
X-RAY DIFFRACTIONr_nbd_other0.1850.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2670.28
X-RAY DIFFRACTIONr_mcbond_it4.7756.4071106
X-RAY DIFFRACTIONr_mcbond_other4.7646.4111105
X-RAY DIFFRACTIONr_mcangle_it7.74311.4851377
X-RAY DIFFRACTIONr_mcangle_other7.7411.4811378
X-RAY DIFFRACTIONr_scbond_it4.8656.741185
X-RAY DIFFRACTIONr_scbond_other4.8646.7411186
X-RAY DIFFRACTIONr_scangle_it7.84312.1391714
X-RAY DIFFRACTIONr_scangle_other7.84112.1381715
X-RAY DIFFRACTIONr_lrange_it11.34861.5652594
X-RAY DIFFRACTIONr_lrange_other11.34961.6012587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6670.274640.274968X-RAY DIFFRACTION99.8066
2.667-2.740.328420.269966X-RAY DIFFRACTION100
2.74-2.8190.265380.251973X-RAY DIFFRACTION100
2.819-2.9060.329350.256911X-RAY DIFFRACTION100
2.906-3.0010.316510.253872X-RAY DIFFRACTION100
3.001-3.1050.338400.228869X-RAY DIFFRACTION100
3.105-3.2220.22400.22829X-RAY DIFFRACTION100
3.222-3.3530.314400.23824X-RAY DIFFRACTION100
3.353-3.5010.286410.221758X-RAY DIFFRACTION100
3.501-3.6710.256290.217755X-RAY DIFFRACTION100
3.671-3.8680.279280.171713X-RAY DIFFRACTION100
3.868-4.1010.19310.163679X-RAY DIFFRACTION100
4.101-4.3810.262290.162628X-RAY DIFFRACTION100
4.381-4.7290.145240.129595X-RAY DIFFRACTION100
4.729-5.1740.164180.134548X-RAY DIFFRACTION99.8236
5.174-5.7750.286330.17497X-RAY DIFFRACTION100
5.775-6.6510.219140.181445X-RAY DIFFRACTION100
6.651-8.1010.3220.152374X-RAY DIFFRACTION100

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