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- PDB-8xx1: The Crystal Structure of MAPKAP kinase 2 domain from Biortus -

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Basic information

Entry
Database: PDB / ID: 8xx1
TitleThe Crystal Structure of MAPKAP kinase 2 domain from Biortus
ComponentsMAP kinase-activated protein kinase 2
KeywordsTRANSFERASE / Kinase Serine/threonine-protein kinase Transferase
Function / homology
Function and homology information


macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calmodulin-dependent protein kinase activity ...macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calmodulin-dependent protein kinase activity / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / regulation of interleukin-6 production / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / Regulation of HSF1-mediated heat shock response / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / MAPK cascade / positive regulation of tumor necrosis factor production / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / 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
MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of MAPKAP kinase 2 domain from Biortus
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
History
DepositionJan 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7151
Polymers36,7151
Non-polymers00
Water3,729207
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)103.239, 103.239, 166.788
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21A-475-

HOH

31A-562-

HOH

41A-595-

HOH

51A-600-

HOH

61A-605-

HOH

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Components

#1: Protein MAP kinase-activated protein kinase 2 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAP-K2 / MAPKAPK-2 / MK-2 / MK2


Mass: 36715.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Production host: Escherichia coli (E. coli)
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.73 Å3/Da / Density % sol: 67.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.1M Sodium malonate dibasic monohydrate, 0.1M HEPES pH 7, 0.5% v/v Jeffamine ED2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.55→49.31 Å / Num. obs: 17831 / % possible obs: 100 % / Redundancy: 21.5 % / CC1/2: 0.998 / Net I/σ(I): 18.2
Reflection shellResolution: 2.55→2.66 Å / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2110 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→49.31 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.869 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.271 / ESU R Free: 0.249
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2454 862 4.843 %
Rwork0.1661 16937 -
all0.17 --
obs-17799 100 %
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: 35.866 Å2
Baniso -1Baniso -2Baniso -3
1--0.464 Å2-0.232 Å2-0 Å2
2---0.464 Å20 Å2
3---1.504 Å2
Refinement stepCycle: LAST / Resolution: 2.55→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 0 207 2590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122438
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162278
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.6573285
X-RAY DIFFRACTIONr_angle_other_deg0.5321.5675334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3685294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.191518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47210473
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.80110112
X-RAY DIFFRACTIONr_chiral_restr0.0730.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_nbd_refined0.2180.2451
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22125
X-RAY DIFFRACTIONr_nbtor_refined0.180.21138
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1160.215
X-RAY DIFFRACTIONr_nbd_other0.250.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.220
X-RAY DIFFRACTIONr_mcbond_it3.9763.6831173
X-RAY DIFFRACTIONr_mcbond_other3.9663.6821173
X-RAY DIFFRACTIONr_mcangle_it6.2095.4951462
X-RAY DIFFRACTIONr_mcangle_other6.2095.4971463
X-RAY DIFFRACTIONr_scbond_it4.5044.1141265
X-RAY DIFFRACTIONr_scbond_other4.5024.1131266
X-RAY DIFFRACTIONr_scangle_it7.3495.9361821
X-RAY DIFFRACTIONr_scangle_other7.3475.9351822
X-RAY DIFFRACTIONr_lrange_it10.09142.6952691
X-RAY DIFFRACTIONr_lrange_other10.07242.5012662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6160.336680.1891201X-RAY DIFFRACTION100
2.616-2.6880.267630.1871185X-RAY DIFFRACTION100
2.688-2.7650.318560.1941155X-RAY DIFFRACTION100
2.765-2.850.251620.1921119X-RAY DIFFRACTION100
2.85-2.9430.284500.1851099X-RAY DIFFRACTION100
2.943-3.0460.295450.1981068X-RAY DIFFRACTION100
3.046-3.1610.267520.1871023X-RAY DIFFRACTION99.9071
3.161-3.2890.27490.183994X-RAY DIFFRACTION99.7132
3.289-3.4350.215440.179955X-RAY DIFFRACTION99.6012
3.435-3.6010.271550.17893X-RAY DIFFRACTION100
3.601-3.7950.151280.14900X-RAY DIFFRACTION100
3.795-4.0240.202420.146823X-RAY DIFFRACTION100
4.024-4.30.195350.145792X-RAY DIFFRACTION100
4.3-4.6410.187400.125735X-RAY DIFFRACTION100
4.641-5.080.246460.138665X-RAY DIFFRACTION100
5.08-5.6720.292410.179616X-RAY DIFFRACTION100
5.672-6.5350.242260.174573X-RAY DIFFRACTION100
6.535-7.9690.192210.145487X-RAY DIFFRACTION100
7.969-11.1250.174260.121391X-RAY DIFFRACTION100
11.125-490.453130.249263X-RAY DIFFRACTION100

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