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- PDB-5dyl: Crystal structure of the cGMP-dependent protein kinase PKG from P... -

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Basic information

Entry
Database: PDB / ID: 5dyl
TitleCrystal structure of the cGMP-dependent protein kinase PKG from Plasmodium Vivax - Apo form
ComponentscGMP-dependent protein kinase, putative
KeywordsTRANSFERASE / Kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cGMP binding / phosphorylation / endoplasmic reticulum membrane / ATP binding / metal ion binding
Similarity search - Function
cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / 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 ...cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / 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 / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
cGMP-dependent protein kinase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWernimont, A.K. / Tempel, W. / He, H. / Seitova, A. / Hills, T. / Neculai, A.M. / Baker, D.A. / Flueck, C. / Kettleborough, C.A. / Arrowsmith, C.H. ...Wernimont, A.K. / Tempel, W. / He, H. / Seitova, A. / Hills, T. / Neculai, A.M. / Baker, D.A. / Flueck, C. / Kettleborough, C.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Hutchinson, A. / El Bakkouri, M. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structures of the cGMP-dependent protein kinase in malaria parasites reveal a unique structural relay mechanism for activation.
Authors: El Bakkouri, M. / Kouidmi, I. / Wernimont, A.K. / Amani, M. / Hutchinson, A. / Loppnau, P. / Kim, J.J. / Flueck, C. / Walker, J.R. / Seitova, A. / Senisterra, G. / Kakihara, Y. / Kim, C. / ...Authors: El Bakkouri, M. / Kouidmi, I. / Wernimont, A.K. / Amani, M. / Hutchinson, A. / Loppnau, P. / Kim, J.J. / Flueck, C. / Walker, J.R. / Seitova, A. / Senisterra, G. / Kakihara, Y. / Kim, C. / Blackman, M.J. / Calmettes, C. / Baker, D.A. / Hui, R.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionNov 4, 2015ID: 4MYI
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.3Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: cGMP-dependent protein kinase, putative


Theoretical massNumber of molelcules
Total (without water)96,7271
Polymers96,7271
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: cGMP-dependent protein kinase, putative

A: cGMP-dependent protein kinase, putative


Theoretical massNumber of molelcules
Total (without water)193,4532
Polymers193,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4310 Å2
ΔGint-4 kcal/mol
Surface area72750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.471, 117.773, 67.682
Angle α, β, γ (deg.)90.000, 94.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein cGMP-dependent protein kinase, putative


Mass: 96726.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_084705 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: A5K0N4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.95 Å3/Da / Density % sol: 68.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 5000 MME, 5% Tacsimate ph7.0, 0.1 M Hepes ph7, 15 mM spermidine, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.4→44.78 Å / Num. obs: 58714 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.064 / Net I/σ(I): 7.7 / Num. measured all: 201478
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.473.40.9071.51553945360.6540.57499.9
10.46-44.783.30.07417.723737260.9820.04897.9

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2551 / WRfactor Rwork: 0.2214 / FOM work R set: 0.771 / SU B: 18.96 / SU ML: 0.207 / SU R Cruickshank DPI: 0.2036 / SU Rfree: 0.2042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 2967 5.1 %RANDOM
Rwork0.2121 ---
obs0.2138 55744 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.25 Å2 / Biso mean: 74.719 Å2 / Biso min: 35.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å2-0 Å20.24 Å2
2---1.3 Å20 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 2.4→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 0 124 6361
Biso mean---50.71 -
Num. residues----802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196409
X-RAY DIFFRACTIONr_bond_other_d0.0010.026105
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9618669
X-RAY DIFFRACTIONr_angle_other_deg0.843313982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0455813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9124.329298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.492151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7571539
X-RAY DIFFRACTIONr_chiral_restr0.0630.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027336
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021505
X-RAY DIFFRACTIONr_mcbond_it1.5652.6873225
X-RAY DIFFRACTIONr_mcbond_other1.56611.7083224
X-RAY DIFFRACTIONr_mcangle_it2.1584.0234026
X-RAY DIFFRACTIONr_rigid_bond_restr1.95736402
X-RAY DIFFRACTIONr_sphericity_bonded6.5556287
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 211 -
Rwork0.328 4094 -
all-4305 -
obs--99.93 %
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)
18.94341.2733-0.75191.587-0.27410.17190.0698-0.814-0.35340.51830.1290.0049-0.0374-0.0077-0.19880.86850.0416-0.27480.72270.12890.6325-6.231432.971543.6512
27.2891-1.54285.50752.0664-1.94489.3645-0.0079-0.9778-0.16720.55250.1925-0.2884-0.26860.0121-0.18460.55190.0015-0.18920.64620.12180.5383-13.567835.15838.9437
31.15490.50980.9522.2741-0.38294.81790.1216-0.07-0.1490.40770.0948-0.44320.50220.2541-0.21630.56290.0422-0.08180.214-0.09490.1957-38.890529.12744.2107
40.07680.55380.29386.92873.25081.5630.02320.1235-0.0224-0.61480.1376-0.3962-0.23930.1873-0.16080.65650.157-0.00280.40670.04470.2193-42.596766.3588-1.9893
513.07180.4271-3.50111.17660.86512.91280.3823-0.61831.65820.11250.2689-0.8388-0.47231.3418-0.65120.8036-0.3465-0.20680.8590.14311.1557-21.162474.185725.4608
63.183-0.3908-0.3533.3624-1.44433.59220.2126-0.0840.21350.2708-0.2933-0.3564-0.130.51970.08070.3969-0.0504-0.07770.1860.01820.0588-34.255555.339930.7763
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 110
2X-RAY DIFFRACTION2A111 - 161
3X-RAY DIFFRACTION3A162 - 361
4X-RAY DIFFRACTION4A362 - 516
5X-RAY DIFFRACTION5A517 - 581
6X-RAY DIFFRACTION6A582 - 816

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