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

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Basic information

Entry
Database: PDB / ID: 6flo
TitleRegulatory subunit of a cAMP-independent protein kinase A from Trypanosoma brucei at 2.1 Angstrom resolution
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
INOSINE / Protein kinase A regulatory subunit / Protein kinase A regulatory subunit
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.138686637 Å
AuthorsVolpato Santos, Y. / Lorentzen, E. / Basquin, J. / Boshart, M.
Funding support Brazil, Germany, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development233134/2014-0 Brazil
German Research FoundationBo1100/7-1 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
DepositionJan 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 10, 2024Group: Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct_ref / struct_ref_seq
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_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)70,0838
Polymers68,8262
Non-polymers1,2576
Water2,342130
1
A: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9493
Polymers34,4131
Non-polymers5362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1345
Polymers34,4131
Non-polymers7214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.460, 71.550, 122.820
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRSERSER(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA219 - 22721 - 29
12ASPASPASPASP(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA229 - 33531 - 137
13ASPASPILEILE(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA337 - 348139 - 150
14ARGARGARGARG(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA350 - 413152 - 215
15GLYGLYHISHIS(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA417 - 451219 - 253
16VALVALASNASN(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA453 - 458255 - 260
17ARGARGLYSLYS(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA460 - 474262 - 276
18THRTHRLYSLYS(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA476 - 488278 - 290
29TYRTYRSERSER(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB219 - 22721 - 29
210ASPASPASPASP(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB229 - 33531 - 137
211ASPASPILEILE(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB337 - 348139 - 150
212ARGARGARGARG(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB350 - 413152 - 215
213GLYGLYHISHIS(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB417 - 451219 - 253
214VALVALASNASN(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB453 - 458255 - 260
215ARGARGLYSLYS(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB460 - 474262 - 276
216THRTHRLYSLYS(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB476 - 488278 - 290

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Components

#1: Protein Protein kinase A regulatory subunit


Mass: 34413.027 Da / Num. of mol.: 2
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, UniProt: Q9GU80*PLUS
#2: Chemical
ChemComp-NOS / INOSINE / Inosine


Mass: 268.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N4O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 32% PEG 3350, 50 mM Tris pH 8.0, 4% MPD, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→49.09 Å / Num. obs: 30014 / % possible obs: 89 % / Redundancy: 4 % / Biso Wilson estimate: 21.3717547556 Å2 / Net I/σ(I): 9.2
Reflection shellResolution: 2.14→2.22 Å / Num. unique obs: 30009

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
BUCCANEERmodel building
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.138686637→49.0836704952 Å / SU ML: 0.371269280305 / Cross valid method: FREE R-VALUE / σ(F): 0.0277024936218 / Phase error: 29.6760677529
RfactorNum. reflection% reflection
Rfree0.274742492489 1998 6.65733706517 %
Rwork0.220238891841 --
obs0.223883743113 30012 89.3320633409 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.0426550602 Å2
Refinement stepCycle: LAST / Resolution: 2.138686637→49.0836704952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 88 130 4514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005720106371144482
X-RAY DIFFRACTIONf_angle_d0.8528454672896094
X-RAY DIFFRACTIONf_chiral_restr0.0484989913175695
X-RAY DIFFRACTIONf_plane_restr0.00456508320636762
X-RAY DIFFRACTIONf_dihedral_angle_d11.22114499972602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1387-2.19220.534745023221800.5532771160831242X-RAY DIFFRACTION55.3601340034
2.1922-2.25140.4490042008471120.414591674011678X-RAY DIFFRACTION75.8474576271
2.2514-2.31770.3924791287891260.3033143198751793X-RAY DIFFRACTION81.9735155916
2.3177-2.39250.3114545939861420.2730397223091863X-RAY DIFFRACTION84.1376416282
2.3925-2.4780.3640946308911280.258841483641943X-RAY DIFFRACTION88.5042735043
2.478-2.57720.3448495631071480.2430154718471988X-RAY DIFFRACTION89.4847088395
2.5772-2.69450.2875663495291510.2322312047112012X-RAY DIFFRACTION90.8441831163
2.6945-2.83650.2856246126771490.2309299966962043X-RAY DIFFRACTION92.5675675676
2.8365-3.01420.2709835995771510.2423009902952125X-RAY DIFFRACTION95.4697986577
3.0142-3.24690.2994083559791530.2265085224262212X-RAY DIFFRACTION98.2142857143
3.2469-3.57360.2665612243161570.1994936256872217X-RAY DIFFRACTION98.3429991715
3.5736-4.09050.2165275445411590.1602425054122224X-RAY DIFFRACTION99.1264559068
4.0905-5.15270.1950961708051680.1396266514152292X-RAY DIFFRACTION99.5951417004
5.1527-49.09660.2100572666761740.1701295434722382X-RAY DIFFRACTION99.6102883866
Refinement TLS params.Method: refined / Origin x: 21.6494457721 Å / Origin y: -12.5074641799 Å / Origin z: 99.1971935704 Å
111213212223313233
T-0.0145814098939 Å20.0152468295041 Å20.183494336358 Å2-0.049165020948 Å2-0.0158532331543 Å2---0.0565203601001 Å2
L0.0809483828147 °2-0.0226684639225 °2-0.0531013411907 °2--0.030022833883 °20.175563258114 °2--0.08929968789 °2
S-0.0441257754618 Å °0.00370709979848 Å °0.14371457232 Å °0.138299645218 Å °-0.00615336465535 Å °-0.113956739444 Å °0.149920343416 Å °-0.0680023481305 Å °8.54241233166E-12 Å °
Refinement TLS groupSelection details: all

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