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- PDB-3ku2: Crystal Structure of inactivated form of CDPK1 from toxoplasma go... -

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Basic information

Entry
Database: PDB / ID: 3ku2
TitleCrystal Structure of inactivated form of CDPK1 from toxoplasma gondii, TGME49.101440
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / cdpks / toxoplasma / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsWernimont, A.K. / Artz, J.D. / Finnerty, P. / Xiao, T. / He, H. / Mackenzie, F. / Sinestera, G. / Hassani, A.A. / Wasney, G. / Vedadi, M. ...Wernimont, A.K. / Artz, J.D. / Finnerty, P. / Xiao, T. / He, H. / Mackenzie, F. / Sinestera, G. / Hassani, A.A. / Wasney, G. / Vedadi, M. / Lourido, S. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Sibley, D.L. / Hui, R. / Lin, Y.H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium.
Authors: Wernimont, A.K. / Artz, J.D. / Finerty, P. / Lin, Y.H. / Amani, M. / Allali-Hassani, A. / Senisterra, G. / Vedadi, M. / Tempel, W. / Mackenzie, F. / Chau, I. / Lourido, S. / Sibley, L.D. / Hui, R.
History
DepositionNov 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,8395
Polymers57,3331
Non-polymers5064
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.010, 72.912, 65.018
Angle α, β, γ (deg.)90.00, 96.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-domain protein kinase 1


Mass: 57333.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1, TGME49_101440 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BJF5
#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.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.97 Å3/Da / Density % sol: 37.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M KF, 2mM AMPPNP, 4 mM MgCl2, 6.25 mM TCEP, 30% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 20008 / Num. obs: 19908 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 56.66 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.048 / Net I/σ(I): 8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.8.0refinement
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hzt

3hzt


Resolution: 2.3→19.97 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.487 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1009 5.09 %RANDOM
Rwork0.1979 ---
all-19889 --
obs-19811 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.2685 Å20 Å20.5026 Å2
2---0.0315 Å20 Å2
3----0.237 Å2
Refine analyzeLuzzati coordinate error obs: 0.309 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 31 78 3654
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.09
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.24 131 4.67 %
Rwork0.209 2673 -
all0.21 2804 -

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