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- PDB-6eh0: Apo crystal structure of the Protein-Kinase A catalytic subunit f... -

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Basic information

Entry
Database: PDB / ID: 6eh0
TitleApo crystal structure of the Protein-Kinase A catalytic subunit from Criteculus
ComponentscAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / apo-structure
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 / cellular response to cold / cAMP-dependent protein kinase / regulation of osteoblast differentiation / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase activity ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cellular response to cold / cAMP-dependent protein kinase / regulation of osteoblast differentiation / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase activity / ciliary base / cAMP-dependent protein kinase complex / protein kinase A signaling / AMP-activated protein kinase activity / protein kinase A regulatory subunit binding / plasma membrane raft / axoneme / mesoderm formation / postsynaptic modulation of chemical synaptic transmission / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / cellular response to glucagon stimulus / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / positive regulation of cholesterol biosynthetic process / neural tube closure / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / peptidyl-serine phosphorylation / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine/threonine kinase activity / protein serine 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. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...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. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
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
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Loewe-Corporation Germany
CitationJournal: Acs Omega / Year: 2019
Title: Conceptional Design of Self-Assembling Bisubstrate-like Inhibitors of Protein Kinase A Resulting in a Boronic Acid Glutamate Linkage
Authors: Mueller, J.M. / Kirschner, R. / Geyer, A. / Klebe, G.
History
DepositionSep 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _entity.formula_weight
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)41,1941
Polymers41,1941
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.684, 72.260, 97.463
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) / Tissue: Ovary / Gene: PRKACA / Organ: Ovary
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P25321, cAMP-dependent protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM Mes-Bis-Tris, 75 mM lithium chloride, 1 mM DTT, 0.1 mM sodium EDTA, 0.25 mM Mega 8, 23% v/v methanol/water in reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.49→42.038 Å / Num. obs: 60102 / % possible obs: 98.9 % / Redundancy: 4.7 % / CC1/2: 1 / Rsym value: 0.038 / Net I/σ(I): 21.26
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 4.46 % / Mean I/σ(I) obs: 2.82 / Num. unique obs: 9392 / CC1/2: 0.894 / Rsym value: 0.493 / % possible all: 96.6

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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 / Resolution: 1.49→42.038 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.92
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 3005 5 %Random selection
Rwork0.1485 ---
obs0.1503 60095 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.49→42.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 0 263 2985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112857
X-RAY DIFFRACTIONf_angle_d1.0753882
X-RAY DIFFRACTIONf_dihedral_angle_d20.9281041
X-RAY DIFFRACTIONf_chiral_restr0.086413
X-RAY DIFFRACTIONf_plane_restr0.008498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4868-1.51110.27191290.1912452X-RAY DIFFRACTION90
1.5111-1.53720.23951400.16862676X-RAY DIFFRACTION99
1.5372-1.56510.20051420.15352692X-RAY DIFFRACTION100
1.5651-1.59530.21141430.13982711X-RAY DIFFRACTION99
1.5953-1.62780.19391410.13662683X-RAY DIFFRACTION99
1.6278-1.66320.18671430.13312712X-RAY DIFFRACTION100
1.6632-1.70190.18511420.12792703X-RAY DIFFRACTION99
1.7019-1.74450.1991420.12682704X-RAY DIFFRACTION100
1.7445-1.79160.19561430.12852699X-RAY DIFFRACTION100
1.7916-1.84440.17971440.13282749X-RAY DIFFRACTION100
1.8444-1.90390.17011420.12982691X-RAY DIFFRACTION99
1.9039-1.97190.17031430.13152715X-RAY DIFFRACTION99
1.9719-2.05090.19091440.14092731X-RAY DIFFRACTION100
2.0509-2.14420.19411430.13962728X-RAY DIFFRACTION100
2.1442-2.25730.16671450.1342754X-RAY DIFFRACTION99
2.2573-2.39870.17281440.13682729X-RAY DIFFRACTION100
2.3987-2.58380.17391450.14712758X-RAY DIFFRACTION99
2.5838-2.84380.18421420.15932706X-RAY DIFFRACTION98
2.8438-3.25520.2061470.16522787X-RAY DIFFRACTION99
3.2552-4.10060.18071470.15792803X-RAY DIFFRACTION99
4.1006-42.05460.1821540.15462907X-RAY DIFFRACTION98

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