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- PDB-6z08: Crystal structure of cAMP-dependent protein kinase A (CHO PKA) in... -

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Basic information

Entry
Database: PDB / ID: 6z08
TitleCrystal structure of cAMP-dependent protein kinase A (CHO PKA) in complex with 4-Nitrophenol
ComponentscAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase
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 / cellular response to cold / regulation of osteoblast differentiation / 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 / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / plasma membrane raft / axoneme / 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 / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / 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 / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
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. / 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. ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
Similarity search - Domain/homology
P-NITROPHENOL / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsOebbeke, M. / Siefker, C. / Heine, A. / Klebe, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts.
Authors: Oebbeke, M. / Siefker, C. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionMay 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2532
Polymers41,1141
Non-polymers1391
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint4 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.650, 71.256, 97.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8 and 23 % methanol (v/v) 0.003 mL drop volume, 0.5 mL reservoir volume Soaking of 4-Nitrophenol ...Details: 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8 and 23 % methanol (v/v) 0.003 mL drop volume, 0.5 mL reservoir volume Soaking of 4-Nitrophenol (10% (v/v) in DMSO) in buffer (60% (v/v)) and MPD (30% (v/v)).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.489→45.614 Å / Num. obs: 58203 / % possible obs: 98 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.92 Å2 / Rsym value: 0.038 / Net I/σ(I): 22.96
Reflection shellResolution: 1.49→1.58 Å / Mean I/σ(I) obs: 2.85 / Num. unique obs: 9369 / Rsym value: 0.502

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F14

6f14


Resolution: 1.49→45.61 Å / SU ML: 0.1421 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.2707
RfactorNum. reflection% reflection
Rfree0.1853 2909 5 %
Rwork0.1614 --
obs0.1626 58191 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.08 Å2
Refinement stepCycle: LAST / Resolution: 1.49→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 10 276 3001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762874
X-RAY DIFFRACTIONf_angle_d0.96363914
X-RAY DIFFRACTIONf_chiral_restr0.0781416
X-RAY DIFFRACTIONf_plane_restr0.0063512
X-RAY DIFFRACTIONf_dihedral_angle_d21.21771051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.25781380.22142611X-RAY DIFFRACTION98.46
1.51-1.540.24241370.2032602X-RAY DIFFRACTION99.28
1.54-1.570.21391390.19722648X-RAY DIFFRACTION99.11
1.57-1.60.19681380.19162619X-RAY DIFFRACTION99.17
1.6-1.630.19791380.17932618X-RAY DIFFRACTION98.29
1.63-1.670.23491370.17892606X-RAY DIFFRACTION97.82
1.67-1.710.2111340.18192547X-RAY DIFFRACTION96.06
1.71-1.750.1771400.16552662X-RAY DIFFRACTION99.72
1.75-1.790.19561410.16672663X-RAY DIFFRACTION99.79
1.79-1.850.20651390.16072646X-RAY DIFFRACTION99.68
1.85-1.910.17341390.15922638X-RAY DIFFRACTION99.28
1.91-1.980.1771390.15492659X-RAY DIFFRACTION99.26
1.98-2.050.15561400.15632655X-RAY DIFFRACTION98.8
2.05-2.150.18531380.1512627X-RAY DIFFRACTION98.05
2.15-2.260.1811370.14642612X-RAY DIFFRACTION97.07
2.26-2.40.1671320.15212504X-RAY DIFFRACTION93.57
2.4-2.590.16951410.15632669X-RAY DIFFRACTION98.25
2.59-2.850.19281400.15772676X-RAY DIFFRACTION98.39
2.85-3.260.18261410.16122674X-RAY DIFFRACTION97.84
3.26-4.110.20151400.14952661X-RAY DIFFRACTION96.85
4.11-45.60.16711410.16772685X-RAY DIFFRACTION92.44
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)
10.323150481199-0.0237066931174-0.03174586598240.7855577058420.2790151247510.2073753331130.05745494016590.037079260897-0.000980956831001-0.122032597487-0.0709640159310.0104076906284-0.1100351988610.0427593279087-0.004557966081540.174901377289-0.01087433868440.008138479733240.1433893769770.002066396134280.14401635921517.764989660912.328928198115.6634170287
20.204353868556-0.154313994933-0.3584005206960.4929180679870.2658639702040.5206193022950.0269885966161-0.00365699701428-0.0190277038687-0.059585897207-0.038064314583-0.0352897277161-0.02419836931880.0225767558196-0.0005867080899540.1169277966720.005763828659090.001027262020820.122767120156-0.005692267660530.12427433185312.26029619479.2121700110524.7668428506
30.670532294262-0.237157036449-0.04975490254830.716500187374-0.1602654393820.7763436675650.0241603012662-0.00761598615920.00279566942907-0.02753964286170.003298475772460.0479505210068-0.0602752779063-0.07854853829160.0002801668300750.09352855150160.0197170968403-0.002502675595030.105599897062-0.005902079077930.1110092225620.13048825346511.49221014933.5389844648
40.242673924425-0.193882931438-0.4650171482870.7156659788730.5116647948740.47814957090.0081228128636-0.00689540781282-0.00449957481915-0.115913293651-0.0156744895039-0.0254446345627-0.06030693354640.02885249539920.01070055183250.122571611348-0.00619871862589-0.001445583181580.1518928936230.01313492980650.15574032212115.06646810674.65440639320.0227392869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 297 )
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 350 )

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