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- PDB-6rsx: Regulatory Subunit of cAMP-dependant Protein Kinase A from Euglen... -

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Basic information

Entry
Database: PDB / ID: 6rsx
TitleRegulatory Subunit of cAMP-dependant Protein Kinase A from Euglena gracilis at 1.6 A resolution
ComponentsRegulatory Subunit of Protein Kinase A (cAMP-dependent) from Euglena gracilis
KeywordsSIGNALING PROTEIN / Protein kinase A / Regulatory Subunit / cAMP / Euglena gracilis
Function / homologyADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Function and homology information
Biological speciesEuglena gracilis (euglena)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVolpato Santos, Y. / Ober, V. / Basquin, J. / Boshart, M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development233134/2014-0 Brazil
CitationJournal: To Be Published
Title: Regulatory Subunit of Protein Kinase A (cAMP-dependent) from Euglena gracilis at 1.6 A resolution
Authors: Volpato Santos, Y. / Ober, V. / Basquin, J. / Boshart, M.
History
DepositionMay 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
A: Regulatory Subunit of Protein Kinase A (cAMP-dependent) from Euglena gracilis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7783
Polymers33,1201
Non-polymers6582
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-5 kcal/mol
Surface area14160 Å2
Unit cell
Length a, b, c (Å)80.586, 80.586, 110.755
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Regulatory Subunit of Protein Kinase A (cAMP-dependent) from Euglena gracilis


Mass: 33119.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Bill Martin laboratory Duesseldorf via Thankgod Ebenezer, Cambridge
Source: (gene. exp.) Euglena gracilis (euglena) / Strain: Z1 / Gene: EG_transcript_11236
Details (production host): synthetic PKAR sequence, codon optimized
Production host: Escherichia coli (E. coli)
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 1) 50mM MES pH 6.0 , 4% MPD , 80mM Ammonium sulfate , 18% PEG 8000 2) 50mM MES pH 6.0, 20% PEG 3350 3) 50mM MES pH 6.0 , 4% MPD , 0.2M Ammonium sulfate , 20% PEG 3350

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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: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→69.79 Å / Num. all: 104899 / Num. obs: 52962 / % possible obs: 99.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 34.7817722306 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.33
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.08069 / Num. unique obs: 7528 / CC1/2: 0.483 / Rrim(I) all: 0.0851

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RGS

1rgs


Resolution: 1.6→69.79 Å / SU ML: 0.314493451728 / Cross valid method: FREE R-VALUE / σ(F): 1.33057047932 / Phase error: 32.3220349819
RfactorNum. reflection% reflection
Rfree0.216302265951 5067 4.87506855114 %
Rwork0.192252314238 --
obs0.193489922461 52599 99.0867057534 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.5093514939 Å2
Refinement stepCycle: LAST / Resolution: 1.6→69.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 44 159 2297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01100161879952282
X-RAY DIFFRACTIONf_angle_d1.084367895283103
X-RAY DIFFRACTIONf_chiral_restr0.0760290362523341
X-RAY DIFFRACTIONf_plane_restr0.00656436908538403
X-RAY DIFFRACTIONf_dihedral_angle_d17.28291777841375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6064-1.62470.5542163009581260.585484624122667X-RAY DIFFRACTION80.0745412844
1.6247-1.64380.636480781821420.5718570045213362X-RAY DIFFRACTION99.3760635281
1.6438-1.66390.5207473284921770.4952158923293242X-RAY DIFFRACTION98.8435964151
1.6639-1.68490.5481152743231740.4609931062893325X-RAY DIFFRACTION99.6014802163
1.6849-1.70710.3880793180871450.4386434647443335X-RAY DIFFRACTION99.3434199258
1.7071-1.73050.3888891840241590.3883146382853339X-RAY DIFFRACTION99.375
1.7305-1.75520.3862823119821680.3552032046263324X-RAY DIFFRACTION99.430523918
1.7552-1.78140.3230520560871400.3202509695753297X-RAY DIFFRACTION99.4502314815
1.7814-1.80920.363983922441710.3201344691493320X-RAY DIFFRACTION99.4870333428
1.8092-1.83890.314938216011340.2786742649873371X-RAY DIFFRACTION99.8575498575
1.8389-1.87060.2727654508191600.2632917863223319X-RAY DIFFRACTION99.9138426192
1.8706-1.90460.2790759651911280.2636444830433326X-RAY DIFFRACTION99.8554495519
1.9046-1.94130.2925518765841700.2507176620123320X-RAY DIFFRACTION99.4868871152
1.9413-1.98090.2772815531521620.2358919215873334X-RAY DIFFRACTION99.8286693318
1.9809-2.0240.2170895958741960.2105301087053304X-RAY DIFFRACTION99.7150997151
2.024-2.0710.2400053352092040.2064275782823306X-RAY DIFFRACTION99.7442455243
2.071-2.12280.2208693315811920.2059065758823304X-RAY DIFFRACTION99.9428244711
2.1228-2.18020.2717126608231720.206524584143310X-RAY DIFFRACTION99.8852553069
2.1802-2.24440.240283255912000.1868887959143320X-RAY DIFFRACTION99.716713881
2.2444-2.31680.2092051925861620.1920476708283273X-RAY DIFFRACTION99.8836871183
2.3168-2.39960.2783041213041520.2144595142873342X-RAY DIFFRACTION100
2.3996-2.49570.2599607680832050.2106701907753253X-RAY DIFFRACTION99.8844598498
2.4957-2.60920.2590647682091680.1977880667753368X-RAY DIFFRACTION100
2.6092-2.74680.2602314356031420.2077620326123348X-RAY DIFFRACTION100
2.7468-2.91890.2175489492631840.2099719811393319X-RAY DIFFRACTION100
2.9189-3.14420.2452869661091700.2092265243793302X-RAY DIFFRACTION100
3.1442-3.46040.216621204041520.1809509956393333X-RAY DIFFRACTION100
3.4604-3.96090.1796656877621940.163087094123334X-RAY DIFFRACTION100
3.9609-4.98910.1561834863222160.1402365687483280X-RAY DIFFRACTION100
4.9891-43.39570.1871958412872020.151697480833293X-RAY DIFFRACTION99.971395881

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