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- PDB-3lij: Crystal structure of full length CpCDPK3 (cgd5_820) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3lij
TitleCrystal structure of full length CpCDPK3 (cgd5_820) in complex with Ca2+ and AMPPNP
ComponentsCalcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
KeywordsTRANSFERASE / calcium dependent protein kinase / EF hand / ATP-binding / Calcium / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein kinase activity / phosphorylation / calcium ion binding / ATP binding
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 / Calcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsQiu, W. / Hutchinson, A. / Wernimont, A. / Walker, J.R. / Sullivan, H. / Lin, Y.-H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Schapira, M. ...Qiu, W. / Hutchinson, A. / Wernimont, A. / Walker, J.R. / Sullivan, H. / Lin, Y.-H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Senisterra, G. / Vedadi, M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Bochkarev, A. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of full length CpCDPK3 (cgd5_820) in complex with Ca2+ and AMPPNP
Authors: Qiu, W. / Hutchinson, A. / Wernimont, A. / Walker, J.R. / Sullivan, H. / Lin, Y.-H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Senisterra, G. / Vedadi, M. / Arrowsmith, ...Authors: Qiu, W. / Hutchinson, A. / Wernimont, A. / Walker, J.R. / Sullivan, H. / Lin, Y.-H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Senisterra, G. / Vedadi, M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Bochkarev, A. / Hui, R. / Amani, M.
History
DepositionJan 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Calcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2667
Polymers56,5751
Non-polymers6916
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.080, 88.060, 58.610
Angle α, β, γ (deg.)90.00, 118.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands


Mass: 56575.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd5_820 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli)
References: UniProt: Q5CS01, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18% PEG3350, 0.1M Ammonium Tartrate, 5 mM CaCl2, 5 mM AMPPNP, 1 mM MgCl2, 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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 18, 2009
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geomet ry
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 40599 / Num. obs: 40219 / % possible obs: 99.1 % / Redundancy: 7.39 % / Biso Wilson estimate: 29.14 Å2 / Rsym value: 0.0483 / Net I/σ(I): 12.45
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.67 % / Mean I/σ(I) obs: 2.63 / Num. unique all: 5955 / Rsym value: 0.4089 / % possible all: 94.4

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Processing

Software
NameVersionClassification
Locallymodified Blu-Ice GUI interface to EPICS controldata collection
BALBESphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.56 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 2013 5.01 %RANDOM
Rwork0.2029 ---
all-40599 --
obs-40168 99.1 %-
Displacement parametersBiso mean: 44.82 Å2
Baniso -1Baniso -2Baniso -3
1--6.7097 Å20 Å2-8.5045 Å2
2--6.4434 Å20 Å2
3---0.2662 Å2
Refine analyzeLuzzati coordinate error obs: 0.288 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 36 252 4040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
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_deg1.01
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2811 142 4.98 %
Rwork0.2518 2707 -
obs-2849 -

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