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- PDB-3coi: Crystal structure of p38delta kinase -

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Basic information

Entry
Database: PDB / ID: 3coi
TitleCrystal structure of p38delta kinase
ComponentsMitogen-activated protein kinase 13P38 mitogen-activated protein kinases
KeywordsTRANSFERASE / Kinase / p38d / p38delta / ERK / MAP kinase / p38-2 / PMK / STK26 / stress-activated protein kinase / structural genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / ATP-binding / Cell cycle / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


cellular response to anisomycin / cellular response to sorbitol / cellular response to sodium arsenite / response to osmotic stress / DSCAM interactions / MAP kinase activity / mitogen-activated protein kinase / cellular response to interleukin-1 / stress-activated MAPK cascade / p38MAPK events ...cellular response to anisomycin / cellular response to sorbitol / cellular response to sodium arsenite / response to osmotic stress / DSCAM interactions / MAP kinase activity / mitogen-activated protein kinase / cellular response to interleukin-1 / stress-activated MAPK cascade / p38MAPK events / NOD1/2 Signaling Pathway / cellular response to hydrogen peroxide / VEGFA-VEGFR2 Pathway / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cellular response to UV / peptidyl-serine phosphorylation / intracellular signal transduction / cell cycle / 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 / Serine/Threonine protein kinases, catalytic 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: 2.09 Å
AuthorsAtwell, S. / Burley, S.K. / Houle, A. / Ramos, A. / Sauder, J.M. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of p38delta kinase.
Authors: Atwell, S. / Burley, S.K. / Houle, A. / Ramos, A. / Sauder, J.M.
History
DepositionMar 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 13


Theoretical massNumber of molelcules
Total (without water)40,6521
Polymers40,6521
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.271, 71.305, 97.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase 13 / P38 mitogen-activated protein kinases / Stress-activated protein kinase 4 / Mitogen-activated protein kinase p38 delta / MAP kinase p38 delta


Mass: 40651.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: HepG2 / Gene: MAPK13, PRKM13, SAPK4 / Plasmid: pSGX4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O15264, mitogen-activated protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TARGET ID NYSGXRC-8325A PROVIDED BY AUTHORS DOES NOT EXIST IN THE TARGET DATABASE.

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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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% Glycerol, 20mM Hepes pH 7.5, 150mM Sodium chloride, 10mM Methionine, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 6, 2003 / Details: KV mirrors
RadiationMonochromator: Kohzu 111 diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.09→35 Å / Num. obs: 27415 / % possible obs: 97.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 10.6
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3318 / Rsym value: 0.627 / % possible all: 82.6

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
EPMRphasing
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OZA

2oza


Resolution: 2.09→35 Å / Isotropic thermal model: Isotropic / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1368 -Random
Rwork0.208 ---
obs0.208 27352 97.3 %-
Refinement stepCycle: LAST / Resolution: 2.09→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 0 175 2933
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.011
X-RAY DIFFRACTIONr_bond_d_na
X-RAY DIFFRACTIONr_bond_d_prot
X-RAY DIFFRACTIONr_angle_refined_deg1.263
X-RAY DIFFRACTIONr_angle_d_na
X-RAY DIFFRACTIONr_angle_d_prot
X-RAY DIFFRACTIONr_angle_deg
X-RAY DIFFRACTIONr_angle_deg_na
X-RAY DIFFRACTIONr_angle_deg_prot
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_d_na
X-RAY DIFFRACTIONr_dihedral_angle_d_prot
X-RAY DIFFRACTIONr_improper_angle_d
X-RAY DIFFRACTIONr_improper_angle_d_na
X-RAY DIFFRACTIONr_improper_angle_d_prot
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it

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