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- PDB-4ofg: Co-crystal structure of carboxy cGMP binding domain of Plasmodium... -

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Basic information

Entry
Database: PDB / ID: 4ofg
TitleCo-crystal structure of carboxy cGMP binding domain of Plasmodium falciparum PKG with cGMP
ComponentsCGMP-dependent protein kinase
KeywordsTRANSFERASE / Phosphate binding cassette/Cyclic GMP binding domain/PKG / Serine/threonine kinase / TF2I / IRAG / cGMP binding
Function / homology
Function and homology information


cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / gamete generation / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / extrinsic component of membrane / cGMP binding / protein kinase A signaling / protein phosphorylation / protein serine kinase activity ...cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / gamete generation / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / extrinsic component of membrane / cGMP binding / protein kinase A signaling / protein phosphorylation / protein serine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum / 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 / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
ETHANOL / PENTANE-1,5-DIAMINE / CYCLIC GUANOSINE MONOPHOSPHATE / 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 Å
AuthorsKim, J.J. / Sanabria figueroa, E. / Kim, C.
CitationJournal: Plos Pathog. / Year: 2015
Title: Crystal Structures of the Carboxyl cGMP Binding Domain of the Plasmodium falciparum cGMP-dependent Protein Kinase Reveal a Novel Capping Triad Crucial for Merozoite Egress.
Authors: Kim, J.J. / Flueck, C. / Franz, E. / Sanabria-Figueroa, E. / Thompson, E. / Lorenz, R. / Bertinetti, D. / Baker, D.A. / Herberg, F.W. / Kim, C.
History
DepositionJan 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,80024
Polymers16,9541
Non-polymers1,84523
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.299, 67.299, 59.518
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CGMP-dependent protein kinase


Mass: 16954.432 Da / Num. of mol.: 1
Fragment: C-terminal cGMP binding domain, UNP residues 401-542
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): delta cya TP2000
References: UniProt: Q8MMZ4, UniProt: Q8I719*PLUS, cGMP-dependent protein kinase

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Non-polymers , 5 types, 73 molecules

#2: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Chemical
ChemComp-N2P / PENTANE-1,5-DIAMINE


Mass: 102.178 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H14N2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 5.5
Details: 0.2 M lithium sulfate, 15% ethanol, 0.1 M citrate at pH 5.5 and 10 % 1,5-diaminopentane dihydrochloride, VAPOR DIFFUSION, temperature 277.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 29, 2012
RadiationMonochromator: Kohzu HDL-4 Double Crystal, Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→26.173 Å / Num. all: 10715 / Num. obs: 10655 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.9 % / Biso Wilson estimate: 17.896 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.03-2.359.60.347.5199.2
2.35-2.9110.13914.8199
2.9-4.2210.90.07927198.1
4.22-12.6410.30.05633.5194.9
12.64-26.178.20.04128.3199.2

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Processing

Software
NameVersionClassification
Specdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→26.173 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.205 541 5.08 %RANDOM
Rwork0.1682 ---
all0.17 10655 --
obs0.17 10655 98.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→26.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 119 50 1344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081314
X-RAY DIFFRACTIONf_angle_d1.1361735
X-RAY DIFFRACTIONf_dihedral_angle_d16.742520
X-RAY DIFFRACTIONf_chiral_restr0.071179
X-RAY DIFFRACTIONf_plane_restr0.005211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.20130.21941360.1722467X-RAY DIFFRACTION98
2.2013-2.51970.21621360.16962500X-RAY DIFFRACTION98
2.5197-3.17360.23471330.18082537X-RAY DIFFRACTION99
3.1736-26.17480.18311360.16092610X-RAY DIFFRACTION97
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)
13.3056-2.22041.01793.74981.47742.41840.05570.3834-0.1522-0.0117-0.1899-0.16550.19540.6090.18420.23670.04550.05760.33550.00080.266932.148231.294825.4995
21.0349-1.60470.71592.5373-0.78864.43060.26820.0305-0.1005-0.0623-0.5725-0.05760.1960.68040.0950.1478-0.09080.03810.4366-0.01160.181630.475641.26713.0028
35.47531.56143.14552.08230.79386.3708-0.1533-0.0627-0.14530.01020.1377-0.01430.13710.4148-0.03890.13620.03010.02650.2210.00110.132124.519937.209424.71
41.09590.22370.62472.42690.41753.6226-0.0809-0.0263-0.2262-0.04620.0150.19890.2686-0.27850.06070.1773-0.0113-0.00330.1977-0.01380.171210.392135.06314.4393
53.0296-3.582.9845.3069-4.81224.46990.26820.5921-0.6142-0.7917-0.25570.10561.13590.2004-0.38850.39140.0068-0.00180.1832-0.05580.222912.988131.82935.1761
63.00523.20860.50665.04281.68084.42040.1321-0.26840.2394-0.32770.02720.22880.3533-0.1204-0.05030.2345-0.0550.00010.2290.02250.20178.510236.3216-0.082
72.50160.1140.9831.4202-1.62673.6393-0.03290.3385-0.0692-0.1510.00920.0753-0.11230.06730.01880.1903-0.00480.00280.1712-0.02680.165113.724939.274110.7949
82.93421.20881.12261.97690.53475.0318-0.15760.06070.0415-0.08120.2047-0.0323-0.26890.2816-0.03930.14650.0007-0.00770.17310.00410.162120.125341.291619.9082
95.1179-1.7343.30381.6386-0.71154.23070.1420.2101-0.2611-0.1888-0.0006-0.0111-0.7741-0.51330.02390.2779-0.0060.03130.30810.01270.176618.227547.52111.5043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 401 through 415 )
2X-RAY DIFFRACTION2chain 'A' and (resid 416 through 423 )
3X-RAY DIFFRACTION3chain 'A' and (resid 424 through 439 )
4X-RAY DIFFRACTION4chain 'A' and (resid 440 through 460 )
5X-RAY DIFFRACTION5chain 'A' and (resid 461 through 467 )
6X-RAY DIFFRACTION6chain 'A' and (resid 468 through 475 )
7X-RAY DIFFRACTION7chain 'A' and (resid 476 through 502 )
8X-RAY DIFFRACTION8chain 'A' and (resid 503 through 519 )
9X-RAY DIFFRACTION9chain 'A' and (resid 520 through 542 )

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