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- PDB-5kbf: cAMP bound PfPKA-R (141-441) -

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Basic information

Entry
Database: PDB / ID: 5kbf
TitlecAMP bound PfPKA-R (141-441)
ComponentsCAMP-dependent protein kinase regulatory subunit, putative
KeywordsTRANSFERASE / Plasmodium falciparum / PKA / protein kinase A / cAMP / CBD / cyclic nucleotide binding / CNB / regulatory domain / R
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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-dependent protein kinase regulatory subunit
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLittler, D.R. / Gilson, P.R. / Crabb, B.S. / Rossjohn, J.J.
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
DepositionJun 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references / Other
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: CAMP-dependent protein kinase regulatory subunit, putative
B: CAMP-dependent protein kinase regulatory subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6146
Polymers69,2982
Non-polymers1,3174
Water64936
1
A: CAMP-dependent protein kinase regulatory subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3073
Polymers34,6491
Non-polymers6582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CAMP-dependent protein kinase regulatory subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3073
Polymers34,6491
Non-polymers6582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.726, 103.797, 104.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CAMP-dependent protein kinase regulatory subunit, putative / cAMP-dependent protein kinase regulatory subunit


Mass: 34648.785 Da / Num. of mol.: 2 / Fragment: UNP residues 144-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PKAr, PF3D7_1223100, PFL1110c / Plasmid: PET28 / Details (production host): hexahis / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): K12 / References: UniProt: Q7KQK0, cAMP-dependent protein kinase
#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein at 12 mg/mL were set in a 1:1 ratio against a reservoir consisting of 20% w/v Polyethylene glycol 3350, 0.1M NaF and 0.1M 1,3-bispropane pH 7.5

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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 315 / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→46.458 Å / Num. obs: 58452 / % possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 8419 / Rpim(I) all: 0.555 / % possible all: 100

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Processing

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

5k8s


Resolution: 2→46.458 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.1 / Stereochemistry target values: ML
Details: DUE TO N-TERMINAL DISORDER THE IDENTITY OF RESIDUES SER-149, VAL-150, SER-151, ALA-152 IS ONLY TENTATIVE.
RfactorNum. reflection% reflection
Rfree0.2854 2951 5.06 %
Rwork0.2454 --
obs0.2474 58355 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→46.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4535 0 88 36 4659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094703
X-RAY DIFFRACTIONf_angle_d1.2566340
X-RAY DIFFRACTIONf_dihedral_angle_d17.7091792
X-RAY DIFFRACTIONf_chiral_restr0.051712
X-RAY DIFFRACTIONf_plane_restr0.004791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03280.37761400.35962624X-RAY DIFFRACTION100
2.0328-2.06790.3621450.35052579X-RAY DIFFRACTION100
2.0679-2.10550.33651330.32572593X-RAY DIFFRACTION100
2.1055-2.1460.30781280.30962605X-RAY DIFFRACTION100
2.146-2.18980.36071230.30922643X-RAY DIFFRACTION100
2.1898-2.23740.32571430.29382582X-RAY DIFFRACTION100
2.2374-2.28940.32261300.2892646X-RAY DIFFRACTION100
2.2894-2.34670.30011380.2852604X-RAY DIFFRACTION100
2.3467-2.41010.32591500.27282610X-RAY DIFFRACTION100
2.4101-2.4810.3191360.28042627X-RAY DIFFRACTION100
2.481-2.56110.34931480.28472613X-RAY DIFFRACTION100
2.5611-2.65260.31041490.28292617X-RAY DIFFRACTION100
2.6526-2.75880.33341480.27122602X-RAY DIFFRACTION100
2.7588-2.88440.30191470.27672641X-RAY DIFFRACTION100
2.8844-3.03640.31361470.27572636X-RAY DIFFRACTION100
3.0364-3.22660.28381460.27822622X-RAY DIFFRACTION100
3.2266-3.47570.33651490.24852648X-RAY DIFFRACTION100
3.4757-3.82530.24821400.22532650X-RAY DIFFRACTION100
3.8253-4.37840.2631310.19842713X-RAY DIFFRACTION100
4.3784-5.5150.20561370.20082712X-RAY DIFFRACTION100
5.515-46.4710.2851430.22362837X-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)
14.23771.18140.97277.0288-2.74225.51930.07310.35020.0944-0.2485-0.6089-0.5505-0.23910.44960.29120.33330.129-0.03290.32120.12580.404480.013367.6988101.4679
22.9433-3.59481.07698.6017-4.41773.4570.55740.8540.3279-0.5622-0.7018-0.5470.31660.65770.20990.4730.17470.07840.50640.20280.482773.091380.279286.7162
34.5513-2.57750.51788.3715-1.80623.1484-0.0944-0.31760.09140.63450.54280.2535-0.16830.046-0.22570.3530.07650.11830.41180.21170.358661.452396.513990.0731
45.30962.297-1.0395.1813-2.03976.6008-0.1762-0.4439-0.5475-0.2824-0.8129-0.65120.31540.88050.54190.43210.18740.03020.60370.3650.572940.924616.177849.4848
53.7849-3.58050.8897.7837-3.45541.9698-0.2864-0.8728-0.30390.2360.77650.05090.0602-0.3171-0.07290.36910.03480.11940.73910.35250.469225.376539.757636.7109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 149 through 291 )
2X-RAY DIFFRACTION2chain 'A' and (resid 292 through 331 )
3X-RAY DIFFRACTION3chain 'A' and (resid 332 through 441 )
4X-RAY DIFFRACTION4chain 'B' and (resid 149 through 291 )
5X-RAY DIFFRACTION5chain 'B' and (resid 292 through 441 )

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