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- PDB-1rgs: REGULATORY SUBUNIT OF CAMP DEPENDENT PROTEIN KINASE -

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Basic information

Entry
Database: PDB / ID: 1rgs
TitleREGULATORY SUBUNIT OF CAMP DEPENDENT PROTEIN KINASE
ComponentsCAMP DEPENDENT PROTEIN KINASE
KeywordsKINASE / REGULATORY SUBUNIT
Function / homology
Function and homology information


PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cardiac muscle cell proliferation ...PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cardiac muscle cell proliferation / cAMP-dependent protein kinase complex / sarcomere organization / Vasopressin regulates renal water homeostasis via Aquaporins / plasma membrane raft / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / axoneme / mesoderm formation / immunological synapse / cAMP binding / cellular response to glucagon stimulus / multivesicular body / regulation of protein phosphorylation / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein domain specific binding / negative regulation of gene expression / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsSu, Y. / Dostmann, W.R.G. / Herberg, F.W. / Durick, K. / Xuong, N.-H. / Ten Eyck, L. / Taylor, S.S. / Varughese, K.I.
CitationJournal: Science / Year: 1995
Title: Regulatory subunit of protein kinase A: structure of deletion mutant with cAMP binding domains.
Authors: Su, Y. / Dostmann, W.R. / Herberg, F.W. / Durick, K. / Xuong, N.H. / Ten Eyck, L. / Taylor, S.S. / Varughese, K.I.
History
DepositionJun 21, 1995Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAMP DEPENDENT PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1523
Polymers32,4941
Non-polymers6582
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.900, 88.900, 179.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein CAMP DEPENDENT PROTEIN KINASE / RI(ALPHA)


Mass: 32493.854 Da / Num. of mol.: 1 / Fragment: REGULATORY SUBUNIT / Mutation: DEL(1-91)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: BOVINE SKELETON MUSCLE / Plasmid: PUC VECTOR / Gene (production host): BOVINE SKELETON MUSCLE / Production host: Escherichia coli (E. coli) / References: UniProt: P00514, EC: 2.7.1.37
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 57 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
20.55-0.6 Mammonium sulfate1drop
35-6.25 %glycerol1drop
45 mMdithiothreitol1drop
540-50 mMsodium acetate1drop
61.1-1.2 Mammonium sulfate1reservoir
710-12.5 %glycerol1reservoir
810 mMdithiothreitol1reservoir
980-100 mMsodium acetate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 6.96 % / Rmerge(I) obs: 0.048
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 16785 / % possible obs: 94 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
UCSDdata reduction
X-PLORphasing
RefinementResolution: 2.8→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.217 -
obs0.217 10254
Displacement parametersBiso mean: 0.212 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 44 0 0 2103
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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