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

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Basic information

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


cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cGMP binding / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / cGMP-dependent protein kinase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsWalker, J.R. / El Bakkouri, M. / Loppnau, P. / Graslund, S. / He, H. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. ...Walker, J.R. / El Bakkouri, M. / Loppnau, P. / Graslund, S. / He, H. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Amani, 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 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / pdbx_struct_oper_list
Item: _audit_author.name / _citation_author.name / _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 1.4Sep 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

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Assembly

Deposited unit
A: cGMP-dependent protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,36213
Polymers96,7271
Non-polymers63612
Water2,540141
1
A: cGMP-dependent protein kinase, putative
hetero molecules

A: cGMP-dependent protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,72426
Polymers193,4532
Non-polymers1,27124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7540 Å2
ΔGint-94 kcal/mol
Surface area73560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.111, 117.906, 67.731
Angle α, β, γ (deg.)90.000, 95.080, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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 (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVX_084705 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: A5K0N4

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Non-polymers , 5 types, 153 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.97 Å3/Da / Density % sol: 69.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18.2% PEG3350, 0.1 M HEPES pH 7.0, 0.1M Succinate, 2mM MgCl2,5mM AMPPNP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 65835 / % possible obs: 99.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.05 / Rrim(I) all: 0.104 / Χ2: 1.237 / Net I/av σ(I): 16.885 / Net I/σ(I): 7 / Num. measured all: 270566
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.383.70.84562860.6980.4750.9730.77895.5
2.38-2.4840.68165420.8020.3790.7810.81299.2
2.48-2.594.20.56966320.8580.3140.6510.813100
2.59-2.734.20.40666110.9060.2230.4640.891100
2.73-2.94.20.25266310.9630.1380.2880.927100
2.9-3.124.20.15866320.9830.0870.1810.989100
3.12-3.444.20.11166550.9890.0610.1271.242100
3.44-3.934.20.08366210.9930.0460.0951.7599.8
3.93-4.954.10.0665950.9950.0340.0692.19899
4.95-504.10.04266300.9970.0240.0481.91697.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4MYI

4myi
PDB Unreleased entry


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.522 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3186 4.8 %RANDOM
Rwork0.2212 ---
obs0.2228 62646 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.4 Å2 / Biso mean: 74.39 Å2 / Biso min: 27.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å20.15 Å2
2---4.14 Å20 Å2
3---2.23 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 0 42 144 6581
Biso mean--79.11 60.97 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196590
X-RAY DIFFRACTIONr_bond_other_d0.0020.026266
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.968909
X-RAY DIFFRACTIONr_angle_other_deg0.917314361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9065823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73624.375304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.706151162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4941540
X-RAY DIFFRACTIONr_chiral_restr0.080.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021540
X-RAY DIFFRACTIONr_mcbond_it0.8112.4743286
X-RAY DIFFRACTIONr_mcbond_other0.8112.4723285
X-RAY DIFFRACTIONr_mcangle_it1.4873.74108
LS refinement shellResolution: 2.302→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 228 -
Rwork0.371 4025 -
all-4253 -
obs--86.06 %
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)
110.88723.7082-0.96021.2686-0.340.24120.20390.0487-0.48970.01420.0235-0.1198-0.02410.0569-0.22730.87060.1482-0.23940.70050.09760.6416-4.69132.81638.73
25.20270.1414.12082.13020.73528.9618-0.0898-0.7856-0.27020.4616-0.008-0.1885-0.04730.60620.09790.61280.1059-0.23760.93740.23180.3351-11.93635.39545.261
30.58060.36680.50012.2268-0.39693.12030.01640.0243-0.06760.35740.0431-0.33030.41950.2159-0.05940.77410.0704-0.06120.4103-0.04660.1168-39.64929.4033.112
40.11210.22230.12655.89842.03860.76030.08890.13350.0481-0.7642-0.0397-0.2967-0.13310.0931-0.04910.91330.08860.0630.49460.05330.1472-41.98668.719-0.677
55.7654-0.3791-0.31792.8132-0.11513.36750.2262-0.10491.03180.2643-0.3418-0.9051-0.63150.95090.11560.7205-0.2192-0.09730.63250.09240.4488-21.43171.46924.953
61.95630.1567-0.41492.2-1.01322.72480.2118-0.13570.02540.2799-0.2142-0.1134-0.05660.28830.00240.7554-0.033-0.10220.46070.00110.0187-36.08253.54632.349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 73
2X-RAY DIFFRACTION2A74 - 162
3X-RAY DIFFRACTION3A163 - 373
4X-RAY DIFFRACTION4A374 - 516
5X-RAY DIFFRACTION5A517 - 617
6X-RAY DIFFRACTION6A618 - 844

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