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- PDB-5n32: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5n32
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 4-chlorobenzyl carbamimidothioate
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


regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cellular response to cold / cAMP-dependent protein kinase / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / sperm capacitation ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cellular response to cold / cAMP-dependent protein kinase / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / cellular response to glucagon stimulus / protein serine/threonine/tyrosine kinase activity / protein kinase A signaling / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-8K5 / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.833 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)43,6295
Polymers43,1072
Non-polymers5223
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-15 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.635, 72.327, 108.531
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: 41113.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylation of S11, 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: 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-8K5 / [azanyl-[(4-chlorophenyl)methylsulfanyl]methylidene]azanium


Mass: 201.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10ClN2S
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.83 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 13, 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: 1.83→50 Å / Num. obs: 41140 / % possible obs: 99.8 % / Redundancy: 6.54 % / CC1/2: 1 / Rrim(I) all: 0.047 / Net I/σ(I): 27.26
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 6.31 % / Mean I/σ(I) obs: 3.74 / Num. unique obs: 6515 / CC1/2: 0.9 / Rrim(I) all: 0.526 / % possible all: 99.4

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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: 1.833→45.548 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 2057 5 %
Rwork0.1876 --
obs0.1889 41138 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.833→45.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 32 157 3042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043056
X-RAY DIFFRACTIONf_angle_d0.6874162
X-RAY DIFFRACTIONf_dihedral_angle_d15.0231814
X-RAY DIFFRACTIONf_chiral_restr0.047449
X-RAY DIFFRACTIONf_plane_restr0.004551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8335-1.87610.28761320.24462507X-RAY DIFFRACTION99
1.8761-1.9230.24871350.22672582X-RAY DIFFRACTION100
1.923-1.9750.27231360.21772567X-RAY DIFFRACTION100
1.975-2.03310.24791350.2122570X-RAY DIFFRACTION100
2.0331-2.09880.25181360.20732592X-RAY DIFFRACTION100
2.0988-2.17380.23891360.19472584X-RAY DIFFRACTION100
2.1738-2.26080.21381360.18532582X-RAY DIFFRACTION100
2.2608-2.36370.22221360.18472581X-RAY DIFFRACTION100
2.3637-2.48830.18931360.18012584X-RAY DIFFRACTION100
2.4883-2.64420.191380.18662613X-RAY DIFFRACTION100
2.6442-2.84830.21281370.19462607X-RAY DIFFRACTION100
2.8483-3.13490.23221380.19852628X-RAY DIFFRACTION100
3.1349-3.58840.20281390.18632637X-RAY DIFFRACTION100
3.5884-4.52030.21161400.16232672X-RAY DIFFRACTION100
4.5203-45.56170.19221470.1852775X-RAY DIFFRACTION99
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)
10.2722-0.3781-0.01060.7435-0.22790.1746-0.1133-0.0728-0.18750.07260.18530.08390.07260.55980.0630.3277-0.0990.10250.4394-0.02520.281-9.31767.9861-1.8796
20.2138-0.1230.18521.3752-0.42850.19660.3320.6084-0.1644-0.6038-0.26530.7250.23510.0430.02760.29180.0223-0.11470.4288-0.03350.4034-19.818218.7319-31.0737
30.6239-0.6467-0.16570.9597-0.0640.26890.06990.04060.08010.0167-0.08070.2991-0.0075-0.20890.00450.2031-0.0386-0.01290.23660.00060.2231-10.869322.0302-18.3754
40.77230.16510.41761.23510.15720.66210.01330.0463-0.0062-0.0144-0.025-0.12230.03040.0207-00.1873-0.0237-0.01160.15670.00770.17233.200618.3426-20.4907
50.42390.49230.37210.74020.2650.47830.1228-0.26170.02050.2246-0.0768-0.12110.08510.0381-0.00310.2823-0.0372-0.00540.24590.01710.17380.666617.798-6.5153
60.828-0.1418-0.63790.5169-0.0471.32510.44450.65260.0182-0.5745-0.02750.2585-0.27910.20851.70550.21580.0973-0.31950.4311-0.0560.3695-18.907623.4322-34.3926
70.0194-0.02560.01570.0362-0.03080.02650.14880.22490.365-0.1905-0.0626-0.18310.01-0.0229-0.00010.2503-0.0075-0.01740.19550.04410.29162.992928.1708-29.6034
80.08590.01960.00730.16270.10610.06920.04280.14830.153-0.2451-0.0683-0.0203-0.00330.2266-0.00870.5879-0.0506-0.02140.4553-0.05360.34441.648913.3174-35.3351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 160 )
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 272 )
5X-RAY DIFFRACTION5chain 'A' and (resid 273 through 316 )
6X-RAY DIFFRACTION6chain 'A' and (resid 317 through 350 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 21 )
8X-RAY DIFFRACTION8chain 'B' and (resid 22 through 27 )

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