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- PDB-5n3g: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5n3g
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule (R)-1,4-oxazepan-6-ol
ComponentscAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / fragment / complex / serine threonine kinase / cAMP / kinase / PKA
Function / homology
Function and homology information


cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation ...cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / acrosomal vesicle / protein export from nucleus / positive regulation of phagocytosis / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / neuromuscular junction / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(6~{R})-1,4-oxazepan-6-ol / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsSiefker, C. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: A crystallographic fragment study with cAMP-dependent protein kinase A
Authors: Siefker, C. / Heine, A. / Klebe, G.
History
DepositionFeb 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Jan 17, 2024Group: 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
Revision 1.3Nov 13, 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: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6645
Polymers41,1941
Non-polymers4714
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-23 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.223, 71.925, 97.733
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 cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 41193.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylation of S140, T198 and S339 / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Chemical ChemComp-8KB / (6~{R})-1,4-oxazepan-6-ol


Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.22 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: MES-BIS-TRIS Mega8-Solution DTT EDTA LiCl Methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2016 / Details: Silicon, active surface
RadiationMonochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.16→50 Å / Num. obs: 124372 / % possible obs: 99.2 % / Redundancy: 5.85 % / CC1/2: 0.99 / Rrim(I) all: 0.059 / Net I/σ(I): 15.1
Reflection shellResolution: 1.16→1.23 Å / Redundancy: 5.65 % / Mean I/σ(I) obs: 2.81 / Num. unique obs: 19767 / CC1/2: 0.86 / Rrim(I) all: 0.566 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WIH

4wih


Resolution: 1.16→45.369 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.11
RfactorNum. reflection% reflection
Rfree0.1567 6219 5 %
Rwork0.1366 --
obs0.1376 124364 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.16→45.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 32 364 3172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113072
X-RAY DIFFRACTIONf_angle_d1.1694180
X-RAY DIFFRACTIONf_dihedral_angle_d21.7471161
X-RAY DIFFRACTIONf_chiral_restr0.09436
X-RAY DIFFRACTIONf_plane_restr0.008541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1597-1.17280.21722010.18413810X-RAY DIFFRACTION98
1.1728-1.18660.20912050.18943907X-RAY DIFFRACTION99
1.1866-1.20110.20872030.17743853X-RAY DIFFRACTION98
1.2011-1.21630.21432050.16973898X-RAY DIFFRACTION99
1.2163-1.23230.18842040.15773882X-RAY DIFFRACTION99
1.2323-1.24920.18372070.15463917X-RAY DIFFRACTION99
1.2492-1.2670.20552040.1533893X-RAY DIFFRACTION99
1.267-1.2860.18562060.14743912X-RAY DIFFRACTION99
1.286-1.30610.19312080.14463938X-RAY DIFFRACTION100
1.3061-1.32750.17142040.13823886X-RAY DIFFRACTION99
1.3275-1.35040.15642060.13333915X-RAY DIFFRACTION99
1.3504-1.37490.15932050.13263898X-RAY DIFFRACTION99
1.3749-1.40140.16882060.12423910X-RAY DIFFRACTION99
1.4014-1.430.15762060.1193911X-RAY DIFFRACTION99
1.43-1.46110.14672070.11283940X-RAY DIFFRACTION100
1.4611-1.49510.13182070.10723922X-RAY DIFFRACTION100
1.4951-1.53240.14392070.10773942X-RAY DIFFRACTION100
1.5324-1.57390.15282080.10773936X-RAY DIFFRACTION100
1.5739-1.62020.15242070.11233945X-RAY DIFFRACTION100
1.6202-1.67250.14082070.11173938X-RAY DIFFRACTION99
1.6725-1.73230.14262050.11533891X-RAY DIFFRACTION98
1.7323-1.80160.12932090.11483963X-RAY DIFFRACTION99
1.8016-1.88360.14612080.12333951X-RAY DIFFRACTION99
1.8836-1.98290.15252080.12863966X-RAY DIFFRACTION100
1.9829-2.10720.12892100.12533991X-RAY DIFFRACTION100
2.1072-2.26990.15662110.12554001X-RAY DIFFRACTION99
2.2699-2.49830.15152070.12833934X-RAY DIFFRACTION98
2.4983-2.85970.15772130.14514042X-RAY DIFFRACTION100
2.8597-3.60270.16442140.15054063X-RAY DIFFRACTION99
3.6027-45.40410.1552210.15624190X-RAY DIFFRACTION98

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