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- PDB-5t3n: Sp-2Cl-cAMPS bound to PKAR CBD2 -

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Basic information

Entry
Database: PDB / ID: 5t3n
TitleSp-2Cl-cAMPS bound to PKAR CBD2
ComponentscAMP-dependent protein kinase regulatory subunit
KeywordsTRANSFERASE / Protein kinase A / PKAR / Plasmodium / cAMP / CBD / CNB / cyclic nucleotide / cyclic adenosine monophosphate
Function / homology
Function and homology information


cAMP-dependent protein kinase regulator activity / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / protein kinase A catalytic subunit binding / cAMP binding / regulation of protein phosphorylation / protein-containing complex ...cAMP-dependent protein kinase regulator activity / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / protein kinase A catalytic subunit binding / cAMP binding / regulation of protein phosphorylation / protein-containing complex / nucleus / cytosol
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / Cyclic nucleotide-binding domain signature 2. / 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 / Jelly Rolls ...cAMP-dependent protein kinase regulatory subunit / Cyclic nucleotide-binding domain signature 2. / 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 / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-75G / IODIDE ION / cAMP-dependent protein kinase regulatory subunit
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLittler, D.R. / Gilson, P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Disrupting the Allosteric Interaction between the Plasmodium falciparum cAMP-dependent Kinase and Its Regulatory Subunit.
Authors: Littler, D.R. / Bullen, H.E. / Harvey, K.L. / Beddoe, T. / Crabb, B.S. / Rossjohn, J. / Gilson, P.R.
History
DepositionAug 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Data collection
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Dec 14, 2016Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-dependent protein kinase regulatory subunit
B: cAMP-dependent protein kinase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4169
Polymers37,0222
Non-polymers1,3947
Water18010
1
A: cAMP-dependent protein kinase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1454
Polymers18,5111
Non-polymers6343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cAMP-dependent protein kinase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2725
Polymers18,5111
Non-polymers7604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.190, 64.190, 195.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-501-

IOD

DetailsFull-length PfPKA is a heterodimer. The current construct does not contain the dimerization interface, so it is monomeric.

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Components

#1: Protein cAMP-dependent protein kinase regulatory subunit


Mass: 18511.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal hexahistidine tag
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PKAr, PF3D7_1223100, PFL1110c / Plasmid: pET-28-NKI-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): DE3 / References: UniProt: Q7KQK0, cAMP-dependent protein kinase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-75G / (2S,4aR,6R,7R,7aS)-6-(6-amino-2-chloro-9H-purin-9-yl)-7-hydroxy-2-sulfanyltetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-2-one / Sp-2-Cl-cAMPS / 2-Chloroadenosine-3', 5'-cyclic monophosphorothioate, Sp-isomer


Mass: 379.717 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11ClN5O5PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% w/v Polethylene glycol 3350, 0.2M NH4I

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 25, 2016 / Details: bragg monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→37.3 Å / Num. obs: 16863 / % possible obs: 99.9 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K8S

5k8s


Resolution: 2.4→33.42 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.08
RfactorNum. reflection% reflection
Rfree0.307 853 5.13 %
Rwork0.251 --
obs0.254 16624 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 51 10 2453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132481
X-RAY DIFFRACTIONf_angle_d2.1793341
X-RAY DIFFRACTIONf_dihedral_angle_d14.77954
X-RAY DIFFRACTIONf_chiral_restr0.113371
X-RAY DIFFRACTIONf_plane_restr0.011420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.55040.38061320.32972546X-RAY DIFFRACTION99
2.5504-2.74720.38021390.33072562X-RAY DIFFRACTION98
2.7472-3.02360.39211360.32622563X-RAY DIFFRACTION98
3.0236-3.46070.33081370.28522618X-RAY DIFFRACTION99
3.4607-4.35860.29061390.22992672X-RAY DIFFRACTION99
4.3586-33.42210.27271700.2132810X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0573-2.9308-1.75264.4542.04742.1553-0.25850.66771.5514-0.41470.5763-0.4155-1.99321.3704-0.33620.9157-0.21580.31320.7419-0.03281.162886.56393.8534-3.305
27.8187-1.2931-4.5280.6280.33873.35581.0167-0.96812.35850.58120.0786-0.3179-2.221.0324-0.93330.7135-0.08950.140.4637-0.14370.760876.335294.84532.4585
39.06192.80784.38293.9719-2.74247.810.5713-0.63220.7831.8169-0.2875-1.5817-0.35470.7198-0.18950.8138-0.131-0.12290.8805-0.43010.965580.391290.413213.722
46.5227-1.8447-5.97724.69713.10799.38720.20550.61780.307-0.0203-0.165-0.2955-0.3409-0.4954-0.13610.33480.05140.04330.2670.05730.374574.545487.04683.747
58.6993-1.4835-1.70614.03611.06388.9836-0.03960.3712-0.37670.0872-0.33090.41260.5382-1.16230.26350.3358-0.07280.06660.3986-0.05970.389462.071185.351816.7634
63.2058-2.9476-3.27263.53953.0043.5799-0.5720.4695-0.5890.17140.18520.32420.5813-0.52580.42940.4970.01220.1570.5768-0.04820.57472.409781.42978.0871
78.19961.9641-4.46843.1605-4.31798.89630.489-2.3794-2.10451.27830.1659-2.4031.67051.9234-0.24680.81730.3771-0.23520.9881-0.03871.073378.43881.270221.6056
87.26890.35730.93343.38744.97687.44560.1053-0.9236-0.94421.5486-0.1313-1.09962.373-0.05580.13340.92980.18820.09960.51360.18360.764167.243181.164430.6662
98.2674.6351.25646.44910.04551.8422-0.05311.3995-1.1998-1.10140.845-1.9913-0.37550.4730.50740.8089-1.55780.46031.2163-0.10731.052471.4189105.190249.5582
104.834-4.68833.1914.5452-3.10572.12370.6498-1.72512.34171.6172-1.466-0.5249-1.00630.28910.30242.117-1.44990.68642.3459-0.44661.437673.5873112.096340.3238
114.7620.6937-0.27325.27531.58436.69470.43720.05320.29520.4768-0.47990.2419-1.8052-0.48540.08660.93260.01210.09550.5453-0.02810.490756.0149102.363735.9259
123.83960.29960.6227.58082.73051.0486-0.27330.04521.0310.3179-0.05770.3337-3.19360.19740.11262.4901-0.3538-0.09180.491-0.05560.744359.1582111.441442.4402
133.84131.9428-0.80263.5971-0.81110.23120.1780.2731.18080.84020.4468-0.3486-1.45960.5417-0.58522.899-0.28880.54891.5725-0.13221.078664.2579115.889229.4894
143.2499-2.55631.81522.408-0.98354.43480.52431.57090.6950.3252-0.3665-0.2923-2.275-1.3485-0.12071.40250.40250.05211.1470.18270.704355.2779108.193819.6089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 287 THROUGH 296 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 297 THROUGH 309 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 310 THROUGH 317 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 318 THROUGH 333 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 334 THROUGH 395 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 396 THROUGH 413 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 414 THROUGH 420 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 421 THROUGH 439 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 294 THROUGH 309 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 310 THROUGH 321 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 322 THROUGH 395 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 396 THROUGH 412 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 413 THROUGH 421 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 422 THROUGH 439 )

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