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- PDB-3ma6: Crystal structure of kinase domain of TgCDPK1 in presence of 3BrB-PP1 -

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Basic information

Entry
Database: PDB / ID: 3ma6
TitleCrystal structure of kinase domain of TgCDPK1 in presence of 3BrB-PP1
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / CDPK / parasitology / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Structural Genomics / Structural Genomics Consortium / SGC
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
Chem-DXR / Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsWernimont, A.K. / Qiu, W. / Amani, M. / Artz, J.D. / Hassani, A.A. / Senisterra, G. / Vedadi, M. / Sibley, L.D. / Lourido, S. / Shokat, K. ...Wernimont, A.K. / Qiu, W. / Amani, M. / Artz, J.D. / Hassani, A.A. / Senisterra, G. / Vedadi, M. / Sibley, L.D. / Lourido, S. / Shokat, K. / Zhang, C. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Hui, R. / Lin, Y.H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of kinase domain of TgCDPK1 in presence of 3BrB-PP1
Authors: Wernimont, A.K. / Qiu, W. / Amani, M. / Artz, J.D. / Hassani, A.A. / Senisterra, G. / Vedadi, M. / Sibley, L.D. / Lourido, S. / Shokat, K. / Zhang, C. / Arrowsmith, C.H. / Edwards, A.M. / ...Authors: Wernimont, A.K. / Qiu, W. / Amani, M. / Artz, J.D. / Hassani, A.A. / Senisterra, G. / Vedadi, M. / Sibley, L.D. / Lourido, S. / Shokat, K. / Zhang, C. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Hui, R. / Lin, Y.H.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,8704
Polymers69,1502
Non-polymers7212
Water1,36976
1
A: Calmodulin-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9352
Polymers34,5751
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calmodulin-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9352
Polymers34,5751
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.329, 145.923, 52.111
Angle α, β, γ (deg.)90.000, 99.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-domain protein kinase 1


Mass: 34574.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1, TGME49_101440 / Plasmid: PET15MLH / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BJF5
#2: Chemical ChemComp-DXR / 3-(3-bromobenzyl)-1-tert-butyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 360.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18BrN5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M Ammonium Formate, 15% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 25619 / Num. obs: 25594 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 63.2 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.052 / Χ2: 1.812 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1272 / Rsym value: 0.626 / Χ2: 2.328 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.82 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.46 Å
Translation2.5 Å48.46 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→34.74 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1293 5.08 %RANDOM
Rwork0.255 ---
all0.257 25628 --
obs0.257 25472 99.39 %-
Displacement parametersBiso max: 189.01 Å2 / Biso mean: 71.798 Å2 / Biso min: 23.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.817 Å20 Å2-1.057 Å2
2---3.906 Å20 Å2
3---2.089 Å2
Refine analyzeLuzzati coordinate error obs: 0.534 Å
Refinement stepCycle: LAST / Resolution: 2.5→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 38 76 4177
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.359 137 4.86 %
Rwork0.335 2681 -
all0.336 2818 -

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