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- PDB-5j3u: Co-crystal structure of the regulatory domain of Toxoplasma gondi... -

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Basic information

Entry
Database: PDB / ID: 5j3u
TitleCo-crystal structure of the regulatory domain of Toxoplasma gondii PKA with cAMP
ComponentsProtein Kinase A
KeywordsTRANSFERASE / Kinase / regulatory domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / kinase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / 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 ...: / 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, putative / Cyclic nucleotide-binding domain-containing protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEl Bakkouri, M. / Walker, J.R. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lin, L. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Co-crystal structure of the regulatory domain of Toxoplasma gondii PKA with cAMP
Authors: El Bakkouri, M. / Walker, J.R. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lin, L.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7945
Polymers28,9511
Non-polymers8434
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.857, 59.414, 120.843
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Protein Kinase A


Mass: 28950.900 Da / Num. of mol.: 1 / Fragment: regulatory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGME49_311300, TGVEG_311300 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: S8EY88, UniProt: A0A0F7V8B2*PLUS, cGMP-dependent protein kinase
#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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% peg3350, 0.1M NH4Oac, 0.1M Hepes pH 7.5, 2 mM cAMP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979337 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979337 Å / Relative weight: 1
ReflectionResolution: 1.8→42.36 Å / Num. obs: 25458 / % possible obs: 100 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.034 / Rrim(I) all: 0.101 / Net I/σ(I): 19.2 / Num. measured all: 221793
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.848.90.8741100
9-42.366.50.03198.8

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OF1, 2QCS, 3TNP

3of1

2qcs

3tnp


Resolution: 1.8→41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.817 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.119
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 1220 4.8 %RANDOM
Rwork0.1696 ---
obs0.1712 24189 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.94 Å2 / Biso mean: 22.494 Å2 / Biso min: 5.45 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.8→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 56 280 2356
Biso mean--21.25 33.39 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192202
X-RAY DIFFRACTIONr_bond_other_d0.0020.022116
X-RAY DIFFRACTIONr_angle_refined_deg1.7852.0052985
X-RAY DIFFRACTIONr_angle_other_deg0.9813.0024819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7195280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.02524.455101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39915393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8141516
X-RAY DIFFRACTIONr_chiral_restr0.1090.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02482
X-RAY DIFFRACTIONr_mcbond_it1.5811.911090
X-RAY DIFFRACTIONr_mcbond_other1.5771.9091089
X-RAY DIFFRACTIONr_mcangle_it2.2252.8521374
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 98 -
Rwork0.233 1762 -
all-1860 -
obs--100 %

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