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- PDB-4myg: MAPK13, active form -

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Basic information

Entry
Database: PDB / ID: 4myg
TitleMAPK13, active form
ComponentsMitogen-activated protein kinase 13
KeywordsTRANSFERASE / p38 kinase / phosphorylation
Function / homology
Function and homology information


cellular response to anisomycin / cellular response to sorbitol / cellular response to sodium arsenite / response to osmotic stress / cellular response to interleukin-1 / MAP kinase activity / mitogen-activated protein kinase / stress-activated MAPK cascade / p38MAPK events / NOD1/2 Signaling Pathway ...cellular response to anisomycin / cellular response to sorbitol / cellular response to sodium arsenite / response to osmotic stress / cellular response to interleukin-1 / MAP kinase activity / mitogen-activated protein kinase / stress-activated MAPK cascade / p38MAPK events / NOD1/2 Signaling Pathway / VEGFA-VEGFR2 Pathway / cellular response to hydrogen peroxide / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cellular response to UV / peptidyl-serine phosphorylation / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase 13 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain ...Mitogen-activated protein kinase 13 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å
AuthorsYurtsever, Z. / Brett, T.J. / Scheaffer, S.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation.
Authors: Yurtsever, Z. / Scheaffer, S.M. / Romero, A.G. / Holtzman, M.J. / Brett, T.J.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 13
B: Mitogen-activated protein kinase 13


Theoretical massNumber of molelcules
Total (without water)85,8642
Polymers85,8642
Non-polymers00
Water3,315184
1
A: Mitogen-activated protein kinase 13


Theoretical massNumber of molelcules
Total (without water)42,9321
Polymers42,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 13


Theoretical massNumber of molelcules
Total (without water)42,9321
Polymers42,9321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.232, 107.232, 125.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Mitogen-activated protein kinase 13 / MAP kinase 13 / MAPK 13 / Mitogen-activated protein kinase p38 delta / MAP kinase p38 delta / ...MAP kinase 13 / MAPK 13 / Mitogen-activated protein kinase p38 delta / MAP kinase p38 delta / Stress-activated protein kinase 4


Mass: 42932.004 Da / Num. of mol.: 2 / Fragment: UNP residues 1-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK13, PRKM13, SAPK4 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: O15264, mitogen-activated protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM Bis-Tris, 21% PEG3350, 200 mM sodium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0007 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 24, 2010
RadiationMonochromator: sagitally focused double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 2.594→50 Å / Num. all: 24975 / Num. obs: 24975 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 48.55 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 19.8
Reflection shellResolution: 2.594→2.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.96 / Rsym value: 0.59 / % possible all: 90.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
BALBESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CM8

1cm8


Resolution: 2.594→49.307 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 1265 5.08 %
Rwork0.2048 --
obs0.2074 24883 97.87 %
all-24884 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.594→49.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5474 0 0 184 5658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055608
X-RAY DIFFRACTIONf_angle_d1.0157594
X-RAY DIFFRACTIONf_dihedral_angle_d13.3972102
X-RAY DIFFRACTIONf_chiral_restr0.039826
X-RAY DIFFRACTIONf_plane_restr0.004966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5935-2.69730.32781130.26172460X-RAY DIFFRACTION91
2.6973-2.82010.30621560.26252553X-RAY DIFFRACTION97
2.8201-2.96880.3351290.24582629X-RAY DIFFRACTION99
2.9688-3.15470.2711660.23992654X-RAY DIFFRACTION99
3.1547-3.39830.28571370.22722634X-RAY DIFFRACTION99
3.3983-3.74010.28681410.20162651X-RAY DIFFRACTION99
3.7401-4.28110.22171390.19252650X-RAY DIFFRACTION99
4.2811-5.39260.24821530.18332652X-RAY DIFFRACTION100
5.3926-49.31580.20111310.18052735X-RAY DIFFRACTION100

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