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- PDB-6h4g: Regulatory subunit of a cAMP-independent protein kinase A from Tr... -

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Basic information

Entry
Database: PDB / ID: 6h4g
TitleRegulatory subunit of a cAMP-independent protein kinase A from Trypanosoma brucei: E311A, T318R, V319A mutant bound to cAMP in the A site
ComponentsProtein kinase A regulatory subunit
KeywordsSIGNALING PROTEIN / Protein kinase A / Regulatory Subunit / Nucleoside-binding protein
Function / homology
Function and homology information


modulation of formation of structure involved in a symbiotic process / cilium movement involved in cell motility / cAMP-dependent protein kinase regulator activity / cAMP-dependent protein kinase complex / cilium / kinase activity / intracellular signal transduction / protein phosphorylation
Similarity search - Function
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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / INOSINE / Protein kinase A regulatory subunit
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14351698698 Å
AuthorsVolpato Santos, Y. / Lorentzen, E. / Basquin, J. / Boshart, M.
Funding support Brazil, Germany, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development Brazil
German Research FoundationBo110/07-1 Germany
CitationJournal: Elife / Year: 2024
Title: Purine nucleosides replace cAMP in allosteric regulation of PKA in trypanosomatid pathogens.
Authors: Ober, V.T. / Githure, G.B. / Volpato Santos, Y. / Becker, S. / Moya Munoz, G. / Basquin, J. / Schwede, F. / Lorentzen, E. / Boshart, M.
History
DepositionJul 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Apr 10, 2024Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,9616
Polymers68,7662
Non-polymers1,1954
Water5,765320
1
A: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9803
Polymers34,3831
Non-polymers5972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9803
Polymers34,3831
Non-polymers5972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.674, 71.197, 121.397
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 Protein kinase A regulatory subunit


Mass: 34383.027 Da / Num. of mol.: 2 / Mutation: E311A, T318R, V319A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb11.02.2210
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q385V6
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical ChemComp-NOS / INOSINE / Inosine


Mass: 268.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N4O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 50 mM Tris pH 8.0 0.2 mM Magnesium Chloride 40% PEG 3350

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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: Nov 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.144→30.21 Å / Num. obs: 31343 / % possible obs: 100 % / Redundancy: 1 % / Biso Wilson estimate: 17.8216436493 Å2 / Rpim(I) all: 0.0888 / Net I/σ(I): 0.92
Reflection shellResolution: 2.144→2.24 Å / Rpim(I) all: 0.1223

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Processing

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

6flo


Resolution: 2.14351698698→30.205523826 Å / SU ML: 0.380726826369 / Cross valid method: FREE R-VALUE / σ(F): 1.34684365027 / Phase error: 31.9468288459
RfactorNum. reflection% reflection
Rfree0.298167135678 2000 6.38202820856 %
Rwork0.23001509224 --
obs0.234430659958 31338 99.5584077263 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.8229744064 Å2
Refinement stepCycle: LAST / Resolution: 2.14351698698→30.205523826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4307 0 82 322 4711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007932201933564532
X-RAY DIFFRACTIONf_angle_d0.9719001614646174
X-RAY DIFFRACTIONf_chiral_restr0.0532435124466695
X-RAY DIFFRACTIONf_plane_restr0.0057111241872780
X-RAY DIFFRACTIONf_dihedral_angle_d17.09680676492644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1435-2.19710.3729521481691360.3247608420431984X-RAY DIFFRACTION95.9710276143
2.1971-2.25650.4293323813421400.3310630266642060X-RAY DIFFRACTION99.7732426304
2.2565-2.32290.3769854373521410.3271238326352063X-RAY DIFFRACTION99.8640688718
2.3229-2.39780.4070999059721410.3145636315492086X-RAY DIFFRACTION99.6420581655
2.3978-2.48350.3825970130261420.2916193965072071X-RAY DIFFRACTION99.9548328817
2.4835-2.58290.3418396686041410.2879461310072085X-RAY DIFFRACTION99.9550965424
2.5829-2.70030.391042438811430.2652706895132084X-RAY DIFFRACTION99.9102736653
2.7003-2.84260.3149776889081410.2495751601372080X-RAY DIFFRACTION99.910031489
2.8426-3.02060.3278639599641430.252622397632089X-RAY DIFFRACTION99.8211091234
3.0206-3.25350.3211277067251430.2262141384532102X-RAY DIFFRACTION99.6449178873
3.2535-3.58050.2729726472931440.1986680225072110X-RAY DIFFRACTION99.8228520815
3.5805-4.09750.2325123158391430.172341057362115X-RAY DIFFRACTION99.9115044248
4.0975-5.15820.1827886869521480.1420430170642159X-RAY DIFFRACTION100
5.1582-30.20850.2334115123871540.1804568811652250X-RAY DIFFRACTION99.6270203067
Refinement TLS params.Method: refined / Origin x: -20.3825618882 Å / Origin y: -12.350172076 Å / Origin z: 23.2982273412 Å
111213212223313233
T0.124489939576 Å20.0134897272553 Å20.0221442434001 Å2-0.104037355961 Å2-0.013929939651 Å2--0.111166913784 Å2
L0.39994516011 °20.0170229466872 °20.0072090674662 °2-0.244836484982 °2-0.231709501538 °2--0.267692289494 °2
S0.0324921355422 Å °0.0569900455677 Å °0.00429306737942 Å °-0.0379963986297 Å °-0.030774109625 Å °0.0131745310207 Å °0.0386194542088 Å °0.0219784576331 Å °0.000579732959136 Å °
Refinement TLS groupSelection details: all

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