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- PDB-5n1h: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5n1h
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule Methyl 4-(aminomethyl)benzoate
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
(4-methoxycarbonylphenyl)methylazanium / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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 6, 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 1.3Oct 23, 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)41,5964
Polymers41,1941
Non-polymers4033
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-22 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.775, 71.730, 97.896
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 S11, S140, T198 and S339 / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Plasmid: pET-16bTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P25321, cAMP-dependent protein kinase
#2: 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
#3: Chemical ChemComp-8G2 / (4-methoxycarbonylphenyl)methylazanium


Mass: 166.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.21 Å3/Da / Density % sol: 44.5 %
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: 1.18→50 Å / Num. obs: 119561 / % possible obs: 99.3 % / Redundancy: 5.81 % / CC1/2: 0.99 / Rrim(I) all: 0.052 / Net I/σ(I): 17.72
Reflection shellResolution: 1.18→1.25 Å / Redundancy: 5.89 % / Mean I/σ(I) obs: 3.44 / Num. unique obs: 18940 / CC1/2: 0.87 / Rrim(I) all: 0.553 / % possible all: 98.5

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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: 1.18→45.768 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1582 5978 5 %
Rwork0.1354 --
obs0.1365 119557 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.18→45.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 28 372 3167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093102
X-RAY DIFFRACTIONf_angle_d1.1324229
X-RAY DIFFRACTIONf_dihedral_angle_d20.8711163
X-RAY DIFFRACTIONf_chiral_restr0.086439
X-RAY DIFFRACTIONf_plane_restr0.008566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1796-1.1930.19141910.17263637X-RAY DIFFRACTION98
1.193-1.20710.20721970.16593748X-RAY DIFFRACTION99
1.2071-1.22180.19851950.15873698X-RAY DIFFRACTION99
1.2218-1.23720.18181970.15423736X-RAY DIFFRACTION99
1.2372-1.25350.17711940.15223700X-RAY DIFFRACTION99
1.2535-1.27070.20611970.14763740X-RAY DIFFRACTION99
1.2707-1.28890.18431970.14693745X-RAY DIFFRACTION99
1.2889-1.30810.16641970.13993734X-RAY DIFFRACTION99
1.3081-1.32850.18561980.13743765X-RAY DIFFRACTION99
1.3285-1.35030.17481970.12983745X-RAY DIFFRACTION99
1.3503-1.37360.14141980.12183758X-RAY DIFFRACTION99
1.3736-1.39860.14891980.11933772X-RAY DIFFRACTION99
1.3986-1.42550.15071970.11853747X-RAY DIFFRACTION100
1.4255-1.45460.17361990.1163763X-RAY DIFFRACTION100
1.4546-1.48620.14821980.11063772X-RAY DIFFRACTION99
1.4862-1.52080.13292000.10363801X-RAY DIFFRACTION100
1.5208-1.55880.12811980.10353762X-RAY DIFFRACTION99
1.5588-1.6010.13611990.10793769X-RAY DIFFRACTION100
1.601-1.64810.14651990.10843785X-RAY DIFFRACTION100
1.6481-1.70130.1432000.11063810X-RAY DIFFRACTION100
1.7013-1.76210.1492000.1133799X-RAY DIFFRACTION100
1.7621-1.83260.14792010.12213818X-RAY DIFFRACTION100
1.8326-1.9160.15771990.1253785X-RAY DIFFRACTION99
1.916-2.01710.1552010.13323812X-RAY DIFFRACTION100
2.0171-2.14340.15712010.13043822X-RAY DIFFRACTION100
2.1434-2.30890.1452030.12683855X-RAY DIFFRACTION100
2.3089-2.54130.15522030.13213849X-RAY DIFFRACTION100
2.5413-2.90890.1662030.15093868X-RAY DIFFRACTION99
2.9089-3.66470.16562070.15613923X-RAY DIFFRACTION100
3.6647-45.80270.15862140.14844061X-RAY DIFFRACTION99

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