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- PDB-5e16: Co-crystal structure of the N-termial cGMP binding domain of Plas... -

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Basic information

Entry
Database: PDB / ID: 5.0E+16
TitleCo-crystal structure of the N-termial cGMP binding domain of Plasmodium falciparum PKG with cGMP
ComponentsCGMP-dependent protein kinase
KeywordsTRANSFERASE / Kinase / cGMP binding domain / 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
CYCLIC GUANOSINE MONOPHOSPHATE / cGMP-dependent protein kinase / cGMP-dependent protein kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsEl Bakkouri, M. / Walker, J.R. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / 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 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Data collection
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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
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 1.4Sep 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: CGMP-dependent protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4232
Polymers16,0781
Non-polymers3451
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.266, 53.847, 92.351
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: 16078.078 Da / Num. of mol.: 1 / Fragment: cGMP binding domain (UNP residues 21-162)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8MMZ4, UniProt: Q8I719*PLUS
#2: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25 % Peg3350, 0.2 M NaCl, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 15745 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Χ2: 1.587 / Net I/av σ(I): 59.607 / Net I/σ(I): 19.4 / Num. measured all: 116330
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.685.60.3037500.9570.1380.3340.88896.8
1.68-1.716.60.2777740.9690.1160.3010.92699.9
1.71-1.747.30.2467770.9780.0970.2650.998100
1.74-1.787.40.2067850.9860.0820.2221.102100
1.78-1.827.40.1737750.9850.0680.1871.229100
1.82-1.867.50.157820.9890.0580.1611.408100
1.86-1.97.50.1357600.9920.0530.1451.439100
1.9-1.967.50.118020.990.0440.1191.587100
1.96-2.017.50.0977560.9960.0380.1041.788100
2.01-2.087.50.0837940.9960.0320.0891.817100
2.08-2.157.60.0717820.9950.0280.0771.836100
2.15-2.247.60.0637840.9980.0240.0671.763100
2.24-2.347.60.0577850.9980.0220.0611.784100
2.34-2.467.70.0517970.9990.0190.0541.613100
2.46-2.627.70.0467790.9990.0170.0491.67499.9
2.62-2.827.70.0437960.9990.0160.0461.735100
2.82-3.117.70.047990.9990.0150.0431.827100
3.11-3.557.60.0377960.9990.0140.0391.863100
3.55-4.487.60.0348200.9990.0130.0372.038100
4.48-506.80.0338520.9990.0130.0352.00197.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MYJ

4myj
PDB Unreleased entry


Resolution: 1.65→46.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.358 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 813 5.2 %RANDOM
Rwork0.1955 ---
obs0.1972 14851 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.65 Å2 / Biso mean: 27.091 Å2 / Biso min: 14.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-0 Å2-0 Å2
2--0.64 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: final / Resolution: 1.65→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 23 104 1205
Biso mean--19.62 36.28 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191170
X-RAY DIFFRACTIONr_bond_other_d0.0020.021091
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9711589
X-RAY DIFFRACTIONr_angle_other_deg0.95132514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80825.3754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89915212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.009155
X-RAY DIFFRACTIONr_chiral_restr0.0930.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021352
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02277
X-RAY DIFFRACTIONr_mcbond_it2.0062.53578
X-RAY DIFFRACTIONr_mcbond_other1.9942.522577
X-RAY DIFFRACTIONr_mcangle_it3.0153.782730
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 53 -
Rwork0.271 1062 -
all-1115 -
obs--95.96 %

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