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

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Basic information

Entry
Database: PDB / ID: 5dyk
TitleCrystal structure of the cGMP-dependent protein kinase PKG from Plasmodium falciparum - Apo form
ComponentsCGMP-dependent protein kinase
KeywordsTRANSFERASE / Kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / gamete generation / extrinsic component of membrane / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / cGMP binding / protein phosphorylation / protein serine kinase activity / endoplasmic reticulum membrane ...cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / gamete generation / extrinsic component of membrane / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / cGMP binding / protein phosphorylation / protein serine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum / signal transduction / ATP binding / metal ion binding / cytoplasm
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 / Jelly Rolls / 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. / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
cGMP-dependent protein kinase / cGMP-dependent protein kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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: 4MYJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct.title
Revision 1.2Nov 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 1.3Sep 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

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Assembly

Deposited unit
A: CGMP-dependent protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3157
Polymers97,8151
Non-polymers5006
Water3,081171
1


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

A: CGMP-dependent protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,63014
Polymers195,6292
Non-polymers1,00112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area5440 Å2
ΔGint-54 kcal/mol
Surface area73640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.509, 127.284, 215.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CGMP-dependent protein kinase


Mass: 97814.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1436600 / Plasmid: pfBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q8MMZ4, UniProt: Q8I719*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.4M L-Proline, 10% Peg 3350, 0.1M Hepes 7.8 15% EG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. obs: 47350 / % possible obs: 96.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.093 / Χ2: 1.123 / Net I/av σ(I): 15.868 / Net I/σ(I): 8.3 / Num. measured all: 223523
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.45-2.494.40.93522530.66993.1
2.49-2.544.70.90322390.64493.2
2.54-2.594.70.77422790.65293.3
2.59-2.644.70.65422590.65794
2.64-2.74.70.56322520.70293.4
2.7-2.764.60.45523120.69294.3
2.76-2.834.70.37822530.72293.9
2.83-2.94.60.32923210.75194.7
2.9-2.994.60.24923230.76995.2
2.99-3.094.60.20423180.85395.8
3.09-3.24.60.16923910.90196.7
3.2-3.324.60.13123681.02497.9
3.32-3.484.60.10624041.17298.2
3.48-3.664.70.08424331.29999.3
3.66-3.894.70.0724101.45599.1
3.89-4.194.80.05824751.61299.7
4.19-4.614.80.05524482.04699.8
4.61-5.274.90.05524922.169100
5.27-6.645.10.05325091.684100
6.64-405.10.03126111.38299.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MYI

4myi
PDB Unreleased entry


Resolution: 2.45→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2236 / WRfactor Rwork: 0.1914 / FOM work R set: 0.8113 / SU B: 17.013 / SU ML: 0.186 / SU R Cruickshank DPI: 0.2209 / SU Rfree: 0.2358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 2346 5.1 %RANDOM
Rwork0.2043 ---
obs0.2061 44059 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.18 Å2 / Biso mean: 51.717 Å2 / Biso min: 25.36 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20 Å2-0 Å2
2--1.31 Å20 Å2
3----3.35 Å2
Refinement stepCycle: final / Resolution: 2.45→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6345 0 30 171 6546
Biso mean--62.91 43.28 -
Num. residues----809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196616
X-RAY DIFFRACTIONr_bond_other_d0.0010.026302
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9668960
X-RAY DIFFRACTIONr_angle_other_deg0.871314462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.485840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03124.595309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.539151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2031539
X-RAY DIFFRACTIONr_chiral_restr0.0670.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021530
X-RAY DIFFRACTIONr_mcbond_it0.8572.1043288
X-RAY DIFFRACTIONr_mcbond_other0.8578.8763287
X-RAY DIFFRACTIONr_mcangle_it1.173.1514119
X-RAY DIFFRACTIONr_rigid_bond_restr1.68936587
X-RAY DIFFRACTIONr_sphericity_bonded4.0256463
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 171 -
Rwork0.274 3051 -
all-3222 -
obs--92.96 %
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)
17.92985.33232.68464.7651.60821.6048-0.1019-0.51830.1178-0.7089-0.06460.5250.0254-0.22790.16650.8547-0.0519-0.07130.73310.14550.55-4.8667-49.738660.7928
25.7443-0.28250.46243.9204-1.69786.61070.3715-0.5666-0.020.0795-0.03430.41170.1258-0.8907-0.33720.5139-0.0473-0.00690.59970.14920.5523-16.4203-49.479354.6409
31.19380.51910.0632.76791.30651.2021-0.1068-0.1269-0.15580.3187-0.00450.04180.0023-0.07680.11130.15540.0579-0.03750.05640.03910.3724-7.417-59.86628.4608
41.26730.976-1.23571.983-1.6472.813-0.0172-0.07030.14010.00460.1211-0.0395-0.19940.1899-0.10390.0669-0.033-0.0510.068-0.03650.40411.4058-49.0603-2.8706
52.2110.5313-0.71152.1326-0.3092.25340.1012-0.22820.26380.2638-0.045-0.2648-0.1450.1359-0.05620.172-0.02-0.07310.0266-0.01080.51413.1744-12.391317.3046
63.3473-0.35070.34042.6935-1.58622.36130.0116-0.28080.05360.28140.05440.0991-0.05090.0552-0.0660.10240.0196-0.0040.0322-0.00850.2903-17.5154-28.77826.8688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 48
2X-RAY DIFFRACTION2A49 - 132
3X-RAY DIFFRACTION3A133 - 251
4X-RAY DIFFRACTION4A252 - 394
5X-RAY DIFFRACTION5A395 - 631
6X-RAY DIFFRACTION6A632 - 853

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