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- PDB-4rgj: Apo crystal structure of CDPK4 from Plasmodium falciparum, PF3D7_... -

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Basic information

Entry
Database: PDB / ID: 4rgj
TitleApo crystal structure of CDPK4 from Plasmodium falciparum, PF3D7_0717500
ComponentsCalcium-dependent protein kinase 4
KeywordsTRANSFERASE / structural genomics / Structural Genomics Consortium / SGC / cdpk / malaria
Function / homology
Function and homology information


calcium-dependent protein serine/threonine phosphatase activity / MAPK6/MAPK4 signaling / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / catalytic activity / cell differentiation / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / protein phosphorylation ...calcium-dependent protein serine/threonine phosphatase activity / MAPK6/MAPK4 signaling / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / catalytic activity / cell differentiation / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / calcium ion binding / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calcium-dependent protein kinase 4
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsWernimont, A.K. / Walker, J.R. / Hutchinson, A. / Seitova, A. / He, H. / Loppnau, P. / Neculai, M. / Amani, M. / Lin, Y.H. / Ravichandran, M. ...Wernimont, A.K. / Walker, J.R. / Hutchinson, A. / Seitova, A. / He, H. / Loppnau, P. / Neculai, M. / Amani, M. / Lin, Y.H. / Ravichandran, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lovato, D.V. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Apo crystal structure of CDPK4 from Plasmodium falciparum, PF3D7_0717500
Authors: Wernimont, A.K. / Walker, J.R. / Hutchinson, A. / Seitova, A. / He, H. / Loppnau, P. / Neculai, M. / Amani, M. / Lin, Y.H. / Ravichandran, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Authors: Wernimont, A.K. / Walker, J.R. / Hutchinson, A. / Seitova, A. / He, H. / Loppnau, P. / Neculai, M. / Amani, M. / Lin, Y.H. / Ravichandran, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lovato, D.V.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-dependent protein kinase 4


Theoretical massNumber of molelcules
Total (without water)59,9961
Polymers59,9961
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.654, 75.548, 92.562
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calcium-dependent protein kinase 4


Mass: 59995.738 Da / Num. of mol.: 1 / Fragment: UNP residues 10-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CDPK4, CPK4, PF07_0072 / Plasmid: DH5-alpha / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q8IBS5, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5% glycerol, 1 mM Nilotinib, 5 mM TCEP, 28% PEG2000 MME, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2014
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.303→56.162 Å / Num. all: 22508 / Num. obs: 22486 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.065 / Χ2: 1.222 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.303-2.346.10.4962.7610920.617100
2.34-2.386.10.43411110.642100
2.38-2.436.10.39211170.671100
2.43-2.486.10.33910750.695100
2.48-2.536.10.30711170.684100
2.53-2.596.10.25211030.76100
2.59-2.656.10.22511090.809100
2.65-2.736.10.18411120.86199.9
2.73-2.816.10.16811170.93699.9
2.81-2.96.10.12711151.024100
2.9-36.10.11411031.158100
3-3.1260.09811201.185100
3.12-3.2660.08211161.39100
3.26-3.4360.0711381.564100
3.43-3.6560.06111241.817100
3.65-3.935.90.05711302.059100
3.93-4.335.80.05311462.424100
4.33-4.955.70.04811452.388100
4.95-6.235.60.04211711.593100
6.23-305.30.02912251.27598.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4QOX

4qox


Resolution: 2.303→56.162 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.195 / FOM work R set: 0.8155 / SU B: 16.225 / SU ML: 0.186 / SU R Cruickshank DPI: 0.3766 / SU Rfree: 0.2531 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.377 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 1123 5 %RANDOM
Rwork0.2014 ---
all0.2041 21427 --
obs0.2041 21316 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.27 Å2 / Biso mean: 53.884 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å2-0 Å20 Å2
2---1.61 Å2-0 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.303→56.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 0 57 3717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193830
X-RAY DIFFRACTIONr_bond_other_d0.0010.023684
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.975169
X-RAY DIFFRACTIONr_angle_other_deg0.75838485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99825.2175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94415725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6791516
X-RAY DIFFRACTIONr_chiral_restr0.0730.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02848
X-RAY DIFFRACTIONr_mcbond_it1.7383.2041906
X-RAY DIFFRACTIONr_mcbond_other1.7363.2021905
X-RAY DIFFRACTIONr_mcangle_it2.8734.7872393
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 66 -
Rwork0.231 1498 -
all-1564 -
obs--95.66 %
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)
12.4857-5.6869-3.168513.49548.21825.99550.41590.0836-0.3918-0.5621-0.50520.72330.336-0.62540.08930.7338-0.10530.00830.72440.03090.90085.9642-30.3083-12.9389
25.2713-1.7683-2.29878.0481.72056.4838-0.00840.0888-0.0514-0.1390.0275-0.1879-0.13040.2633-0.01910.13410.00990.02360.13470.01650.1476-4.4703-14.6799-6.377
33.94631.8528-1.20952.8656-1.63772.9818-0.42660.8251-0.0554-0.32660.4729-0.0126-0.0377-0.4684-0.04630.1859-0.040.02120.2827-0.02720.1098-15.3019-24.7032-4.8704
42.7096-1.21190.11571.8677-0.82183.326-0.0161-0.11190.0620.0343-0.1945-0.2342-0.15430.08930.21060.16640.0103-0.02050.0597-0.00340.1984-6.3312-32.50119.875
52.9339-0.1259-0.96862.4332-0.25462.6502-0.2463-0.0753-0.5517-0.0199-0.0998-0.00080.23280.11840.34610.15390.05550.02990.03340.04560.245-5.401-46.001512.3545
60.5318-0.04750.49983.13-2.32132.99570.0182-0.0113-0.1105-0.14610.0167-0.16030.1455-0.1879-0.0350.15950.01570.03140.0815-0.01630.117715.393-31.194-15.6009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 57
2X-RAY DIFFRACTION2A58 - 100
3X-RAY DIFFRACTION3A101 - 150
4X-RAY DIFFRACTION4A151 - 231
5X-RAY DIFFRACTION5A232 - 355
6X-RAY DIFFRACTION6A356 - 528

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