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- PDB-4ieb: Crystal Structure of a Gly128Met mutant of the toxoplasma CDPK, T... -

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Basic information

Entry
Database: PDB / ID: 4ieb
TitleCrystal Structure of a Gly128Met mutant of the toxoplasma CDPK, TGME49_101440
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / cdpks / toxoplasma / kinase / protist / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase
Function / homology
Function and homology information


phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsWernimont, A.K. / Artz, J.D. / El Bakkouri, M. / Schapira, M. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of a Gly128Met mutant of the toxoplasma CDPK, TGME49_101440
Authors: Wernimont, A.K. / Artz, J.D. / El Bakkouri, M. / Schapira, M. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Hui, R. / Amani, M.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1456
Polymers58,4781
Non-polymers6675
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.174, 96.684, 102.360
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 Calmodulin-domain protein kinase 1 / Calmodulin-domain protein kinase / putative


Mass: 58478.352 Da / Num. of mol.: 1 / Mutation: G128M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1, TGGT1_059880, TGME49_101440, TGVEG_042030 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 14% PEG3350, 0.3 M MgAcetate, 0.1 M Glycine pH 9.5, 5 mM CaCl2, 2 mM MgCl2, 5 mM AMPPNP, 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: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 32213 / Num. obs: 31956 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.383 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.05-2.095.50.2556.5713651.20486.1
2.09-2.126.70.2269.2115581.12499.9
2.12-2.167.30.20115821.10699.9
2.16-2.217.30.1616021.069100
2.21-2.267.30.17415691.47599.6
2.26-2.317.30.14915801.261100
2.31-2.377.40.12216021.02100
2.37-2.437.30.10115961.0799.9
2.43-2.57.30.09115861.052100
2.5-2.587.40.08415941.055100
2.58-2.687.30.07415891.086100
2.68-2.787.30.06516111.099100
2.78-2.917.30.05815771.151100
2.91-3.067.30.0516131.18999.9
3.06-3.257.20.04716151.38799.9
3.25-3.517.10.04516231.63599.9
3.51-3.8670.04716332.15799.9
3.86-4.426.90.04916342.59299.9
4.42-5.566.80.04416742.12199.9
5.56-506.40.0417531.85598.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.34 Å
Translation2.5 Å48.34 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→48.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2151 / WRfactor Rwork: 0.1722 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8523 / SU B: 8.072 / SU ML: 0.114 / SU R Cruickshank DPI: 0.2011 / SU Rfree: 0.1679 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 1613 5.1 %RANDOM
Rwork0.1743 ---
obs0.1765 31878 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.9 Å2 / Biso mean: 27.759 Å2 / Biso min: 6.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å2-0 Å2
2---0.6 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 35 321 4082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193909
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9845296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.525487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73324.722180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00815707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6541521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022886
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 126 -
Rwork0.199 2155 -
all-2281 -
obs--97.52 %
Refinement TLS params.Method: refined / Origin x: 20.995 Å / Origin y: -0.9 Å / Origin z: -6.9889 Å
111213212223313233
T0.0145 Å20.0027 Å20.0082 Å2-0.0794 Å2-0.0002 Å2--0.0249 Å2
L0.2923 °2-0.3369 °20.1525 °2-1.1482 °2-0.5447 °2--0.6639 °2
S-0.0009 Å °0.0118 Å °-0.0014 Å °0.0026 Å °0.0032 Å °-0.041 Å °-0.0753 Å °-0.0014 Å °-0.0023 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 508
2X-RAY DIFFRACTION1A601 - 604

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