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- PDB-5n1o: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5n1o
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 2-chloro-4-(chloromethyl)-5-hydroxyphenyl)ethan-1-one
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase inhibitor alpha-like protein
KeywordsTRANSFERASE / fragment / complex / serine threonine kinase / cAMP / kinase / PKA
Function / homology
Function and homology information


negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus ...negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / 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 / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / positive regulation of gluconeogenesis / acrosomal vesicle / positive regulation of phagocytosis / protein export from nucleus / 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 / positive regulation of insulin secretion / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / 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 / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / 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 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / 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
Chem-8GB / cAMP-dependent protein kinase inhibitor / UPF0418 protein FAM164A / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Jan 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 1.2Oct 16, 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
B: cAMP-dependent protein kinase inhibitor alpha-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5244
Polymers43,1872
Non-polymers3372
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-15 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.081, 71.904, 108.946
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
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: Protein/peptide cAMP-dependent protein kinase inhibitor alpha-like protein


Mass: 1993.318 Da / Num. of mol.: 1 / Fragment: UNP residues 12-30 / Source method: obtained synthetically / Details: cAMP dependent protein kinase inhibitor peptide / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: A0A061IH64, UniProt: G3HK48*PLUS
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-8GB / 1-[5-chloranyl-3-(chloromethyl)-2-oxidanyl-phenyl]ethanone


Mass: 219.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8Cl2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.85 Å3/Da / Density % sol: 57 %
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: Mar 12, 2016 / Details: Silicon, active surface
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 43882 / % possible obs: 99.6 % / Redundancy: 7.24 % / CC1/2: 0.99 / Rrim(I) all: 0.091 / Net I/σ(I): 23
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.58 / Num. unique obs: 6860 / CC1/2: 0.92 / % possible all: 97.9

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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: 1.8→45.648 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.21
RfactorNum. reflection% reflection
Rfree0.1911 2195 5 %
Rwork0.1712 --
obs0.1722 43878 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→45.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 21 194 2991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152909
X-RAY DIFFRACTIONf_angle_d1.2873960
X-RAY DIFFRACTIONf_dihedral_angle_d14.6121706
X-RAY DIFFRACTIONf_chiral_restr0.071426
X-RAY DIFFRACTIONf_plane_restr0.01518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7957-1.83480.27971290.24622437X-RAY DIFFRACTION95
1.8348-1.87740.21551350.20992567X-RAY DIFFRACTION100
1.8774-1.92440.23781340.19362551X-RAY DIFFRACTION100
1.9244-1.97640.24641370.18232606X-RAY DIFFRACTION100
1.9764-2.03460.21051360.17562580X-RAY DIFFRACTION100
2.0346-2.10030.21231370.16812592X-RAY DIFFRACTION100
2.1003-2.17530.17451370.16742603X-RAY DIFFRACTION100
2.1753-2.26240.20871350.15852580X-RAY DIFFRACTION100
2.2624-2.36540.17011360.15732588X-RAY DIFFRACTION100
2.3654-2.49010.19021360.15762583X-RAY DIFFRACTION100
2.4901-2.64610.19131380.16712623X-RAY DIFFRACTION100
2.6461-2.85040.211380.17332603X-RAY DIFFRACTION100
2.8504-3.13710.20741390.1742644X-RAY DIFFRACTION100
3.1371-3.59090.20781390.17412653X-RAY DIFFRACTION100
3.5909-4.52360.16471410.15232678X-RAY DIFFRACTION100
4.5236-45.66290.17051480.18392795X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8605-1.18990.27451.6635-0.31840.2324-0.0294-0.4535-0.33790.47040.60340.59020.21430.45160.45750.3411-0.11160.09440.5232-0.00170.4523-11.69626.6695-3.4849
20.5902-0.10370.07731.413-0.13770.37390.16530.6251-0.0403-0.57960.10520.83170.2618-0.42560.08470.346-0.0697-0.10930.58210.05780.5503-21.906122.145-31.3175
31.0892-0.79750.00721.3756-0.83450.87050.13030.1275-0.0078-0.058-0.00820.41190.0323-0.28140.0160.2557-0.033-0.02310.31050.00130.2619-11.049219.8263-20.5609
40.9570.12090.12831.68780.06430.79150.01590.11150.0215-0.0868-0.0196-0.1838-0.0095-0.032200.2386-0.0275-0.00410.20590.01080.22681.386917.6206-22.5
50.95920.41750.26330.9827-0.34921.3729-0.0608-0.27760.04040.45930.032-0.1540.04390.1272-0.00270.3346-0.0424-0.0420.23260.01210.24273.842220.2488-7.6235
60.34710.0854-0.33710.9546-0.05670.78790.32990.48230.0916-0.3872-0.02980.2740.0162-0.1931.25770.32480.0383-0.18490.53720.01660.4075-18.894223.9291-34.3956
70.5073-0.333-0.11090.20870.05120.07960.35150.23820.0961-0.6527-0.2051-0.23390.071-0.06620.03280.37670.0149-0.02310.28050.0410.30632.133824.6034-31.0199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 160 )
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 252 )
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 316 )
6X-RAY DIFFRACTION6chain 'A' and (resid 317 through 350 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 25 )

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