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- PDB-6ftf: Regulatory subunit of a cAMP-independent protein kinase A from Tr... -

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Basic information

Entry
Database: PDB / ID: 6ftf
TitleRegulatory subunit of a cAMP-independent protein kinase A from Trypanosoma cruzi at 1.09 A resolution
ComponentsProtein kinase A regulatory subunit, putative
KeywordsSIGNALING PROTEIN / protein kinase A / regulatory subunit / cell signalling
Function / homology
Function and homology information


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 / RmlC-like jelly roll fold / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
7-cyano-7-deazainosine / Protein kinase A regulatory subunit, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09151939067 Å
AuthorsVolpato Santos, Y. / Lorentzen, E. / Basquin, J. / Boshart, M.
Funding support Brazil, Germany, 2items
OrganizationGrant numberCountry
CNPq/CsF Brazil
German Research FoundationBo1100/7-1 Germany
CitationJournal: Nat Commun / Year: 2019
Title: Nucleoside analogue activators of cyclic AMP-independent protein kinase A of Trypanosoma.
Authors: Bachmaier, S. / Volpato Santos, Y. / Kramer, S. / Githure, G.B. / Klockner, T. / Pepperl, J. / Baums, C. / Schenk, R. / Schwede, F. / Genieser, H.G. / Dupuy, J.W. / Forne, I. / Imhof, A. / ...Authors: Bachmaier, S. / Volpato Santos, Y. / Kramer, S. / Githure, G.B. / Klockner, T. / Pepperl, J. / Baums, C. / Schenk, R. / Schwede, F. / Genieser, H.G. / Dupuy, J.W. / Forne, I. / Imhof, A. / Basquin, J. / Lorentzen, E. / Boshart, M.
History
DepositionFeb 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein kinase A regulatory subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2476
Polymers34,4761
Non-polymers7715
Water8,647480
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, It was confirmed by SEC that this truncation of the protein is a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint8 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.846, 89.066, 45.634
Angle α, β, γ (deg.)90.000, 98.182, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Protein kinase A regulatory subunit, putative


Mass: 34476.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053506227.150
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): Rosetta / References: UniProt: Q4DSV5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-7CI / 7-cyano-7-deazainosine


Mass: 292.247 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C12H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.82 %
Description: Most of the crystals grew in plates that poorly diffracted to 3 Angstrons , nevertheless after searching in many drops we could find more tridimensional crystals that diffracted up to 1 Angstrom
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Elution buffer (Size Exclusion): 50 mM Hepes pH 7.5, 50 mM NaCl, 1 mM DMSO Crystallization buffer: 17% PEG 6.000, 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→40.4 Å / Num. obs: 215190 / % possible obs: 81.3 % / Redundancy: 3.48 % / Biso Wilson estimate: 10.9897840654 Å2 / Net I/σ(I): 11.28
Reflection shellResolution: 1.092→1.131 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FLO

6flo


Resolution: 1.09151939067→40.4 Å / SU ML: 0.0898747422135 / Cross valid method: FREE R-VALUE / Phase error: 17.5736458365
Details: The data are >97% complete to 1.4A resolution. The low over all completeness is due to 68% completeness in the highest resolution shell (1.4-1.1A resolution
RfactorNum. reflection% reflection
Rfree0.159859886456 2000 1.82999359502 %
Rwork0.150397880586 --
obs0.150566354651 109290 81.8455501303 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.3294899896 Å2
Refinement stepCycle: LAST / Resolution: 1.09151939067→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 54 480 2830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009140978670112521
X-RAY DIFFRACTIONf_angle_d1.053286606833440
X-RAY DIFFRACTIONf_chiral_restr0.374613677346389
X-RAY DIFFRACTIONf_plane_restr0.0067036751346440
X-RAY DIFFRACTIONf_dihedral_angle_d20.4064454927930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0915-1.11880.294345463749620.2738429228823314X-RAY DIFFRACTION35.6306068602
1.1188-1.14910.268070864482810.2437587136864339X-RAY DIFFRACTION46.3993281545
1.1491-1.18290.2229165793281130.2227571987256070X-RAY DIFFRACTION65.1184834123
1.1829-1.22110.2148467727321330.2130380217837144X-RAY DIFFRACTION76.4471057884
1.2211-1.26470.1984581387211400.1990259414277541X-RAY DIFFRACTION80.6065694197
1.2647-1.31540.193293004521460.1885886840797825X-RAY DIFFRACTION83.5359463425
1.3154-1.37520.1952498487651540.1812887785158230X-RAY DIFFRACTION88.1227664494
1.3752-1.44770.1824482853021570.1667889903558463X-RAY DIFFRACTION90.6795707974
1.4477-1.53840.1675153560221630.1519084744988712X-RAY DIFFRACTION93.0976607574
1.5384-1.65720.1553672205471660.1420582358818900X-RAY DIFFRACTION95.1711106446
1.6572-1.8240.1362982988161680.1413450758369054X-RAY DIFFRACTION96.3133159269
1.824-2.08790.1545323774271700.1360710780139109X-RAY DIFFRACTION97.1216244505
2.0879-2.63050.1446486457031720.1373096486379200X-RAY DIFFRACTION97.9924717691
2.6305-44.57010.1470788227081750.1382080708799389X-RAY DIFFRACTION98.9959631508
Refinement TLS params.Method: refined / Origin x: -38.1723037237 Å / Origin y: 86.9790978427 Å / Origin z: 63.5542836084 Å
111213212223313233
T0.0704159678563 Å20.00283531016019 Å2-0.00215399651564 Å2-0.0628207465125 Å2-0.0069517337931 Å2--0.0567405539019 Å2
L0.338124862915 °20.0922346736372 °2-0.0281506369245 °2-0.400602047252 °2-0.251081397043 °2--0.242901152708 °2
S0.0031115017437 Å °0.0108923862725 Å °0.003053850139 Å °0.0112768471593 Å °0.0307312010139 Å °0.0187090548114 Å °0.0123477432194 Å °-0.0110298923265 Å °0.029872760259 Å °
Refinement TLS groupSelection details: all

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