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- PDB-1fot: STRUCTURE OF THE UNLIGANDED CAMP-DEPENDENT PROTEIN KINASE CATALYT... -

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Basic information

Entry
Database: PDB / ID: 1fot
TitleSTRUCTURE OF THE UNLIGANDED CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT FROM SACCHAROMYCES CEREVISIAE
ComponentsCAMP-DEPENDENT PROTEIN KINASE TYPE 1
KeywordsTRANSFERASE / cAMP-dependent Protein Kinase / open conformation / protein kinase
Function / homology
Function and homology information


PKA activation / PKA activation in glucagon signalling / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / CREB1 phosphorylation through the activation of Adenylate Cyclase / Hedgehog 'off' state / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / negative regulation of cytoplasmic mRNA processing body assembly / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells ...PKA activation / PKA activation in glucagon signalling / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / CREB1 phosphorylation through the activation of Adenylate Cyclase / Hedgehog 'off' state / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / negative regulation of cytoplasmic mRNA processing body assembly / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / : / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / regulation of macroautophagy / double-strand break repair via nonhomologous end joining / protein import into nucleus / Ras protein signal transduction / protein kinase activity / cell division / protein serine kinase activity / chromatin / signal transduction / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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
cAMP-dependent protein kinase type 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsMashhoon, N. / Carmel, G. / Pflugrath, J.W. / Kuret, J.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2001
Title: Structure of the unliganded cAMP-dependent protein kinase catalytic subunit from Saccharomyces cerevisiae.
Authors: Mashhoon, N. / Carmel, G. / Pflugrath, J.W. / Kuret, J.
#1: Journal: Biochemistry / Year: 1991
Title: Crystallization and Preliminary X-ray Analysis of the cAMP-Depende Protein Kinase Catalytic Subunit from Saccharomyces cerevisiae
Authors: Kuret, J. / Pflugrath, J.W.
History
DepositionAug 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Aug 14, 2019Group: Data collection / Category: computing
Revision 1.7Oct 9, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAMP-DEPENDENT PROTEIN KINASE TYPE 1


Theoretical massNumber of molelcules
Total (without water)37,4151
Polymers37,4151
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.000, 61.000, 322.000
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 TYPE 1 / TPK1 DELTA


Mass: 37414.500 Da / Num. of mol.: 1 / Fragment: N-TERMINUS TRUNCATED TPK1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: SACCHAROMYCES CEREVISIAE / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06244, EC: 2.7.1.37
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 9

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris-HCl, Propanol, MgCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Details: Kuret, J., (1991) Biochemistry, 30, 10595.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
210 %2-propanol1drop
310 mM1dropMgCl2

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→98 Å / Num. all: 9224 / Num. obs: 7854 / % possible obs: 82.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / Biso Wilson estimate: 76.4 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 2.8→2.97 Å / Num. unique all: 801 / % possible all: 52.7
Reflection
*PLUS
Num. measured all: 86072
Reflection shell
*PLUS
% possible obs: 52.7 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
X-PLORrefinement
PHASESphasing
MADNESSdata reduction
FSdata scaling
PROTEINdata scaling
RefinementResolution: 2.8→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3942096.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: CNS 0.5 standard tables
RfactorNum. reflection% reflectionSelection details
Rfree0.243 828 10.5 %RANDOM
Rwork0.194 ---
obs0.194 7854 82.1 %-
all-8682 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.54 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso mean: 50.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å26.3 Å20 Å2
2---0.63 Å20 Å2
3---1.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.57 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 0 2 2497
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.43
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.231.5
X-RAY DIFFRACTIONc_mcangle_it6.352
X-RAY DIFFRACTIONc_scbond_it7.582
X-RAY DIFFRACTIONc_scangle_it10.062.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 80 10 %
Rwork0.31 721 -
obs--52.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3THP.PARTHP.TOP
Software
*PLUS
Name: 'X-PLOR AND CNS 0.5' / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 50.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg4.43
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.384 / % reflection Rfree: 10 % / Rfactor Rwork: 0.31

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