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- PDB-3l19: Crystal structure of calcium binding domain of CpCDPK3, cgd5_820 -

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Basic information

Entry
Database: PDB / ID: 3l19
TitleCrystal structure of calcium binding domain of CpCDPK3, cgd5_820
ComponentsCalcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
KeywordsTRANSFERASE / calcium dependent protein kinase / EF hand / calmodulin / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...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 / 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
Similarity search - Domain/homology
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: 2.14 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 calcium binding domain of CpCDPK3, cgd5_820
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
DepositionDec 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 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 / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
B: Calcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,35315
Polymers48,4262
Non-polymers92713
Water2,432135
1
A: Calcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
hetero molecules

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)48,93012
Polymers48,4262
Non-polymers50510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4250 Å2
ΔGint-115 kcal/mol
Surface area20200 Å2
MethodPISA
2
B: Calcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)49,77518
Polymers48,4262
Non-polymers1,35016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4010 Å2
ΔGint-120 kcal/mol
Surface area19970 Å2
MethodPISA
3
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)24,4656
Polymers24,2131
Non-polymers2525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Calcium/calmodulin dependent protein kinase with a kinase domain and 4 calmodulin like EF hands
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8889
Polymers24,2131
Non-polymers6758
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.570, 64.187, 72.807
Angle α, β, γ (deg.)90.00, 97.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 24212.820 Da / Num. of mol.: 2
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.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG550MME, 0.05M Magnesium Chloride, 0.1M Hepes, 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: 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: 2.14→50 Å / Num. all: 23334 / Num. obs: 22779 / % possible obs: 97.5 % / Redundancy: 7.39 % / Biso Wilson estimate: 39.16 Å2 / Rmerge(I) obs: 0.0692 / Rsym value: 0.0351 / Net I/σ(I): 17.88
Reflection shellResolution: 2.14→2.19 Å / Redundancy: 6.58 % / Rmerge(I) obs: 0.5951 / Mean I/σ(I) obs: 2.99 / Num. unique all: 946 / Rsym value: 0.5065 / % possible all: 85.8

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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
Starting model: pdb entry 2aao

2aao


Resolution: 2.14→19.35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 1168 5.13 %RANDOM
Rwork0.2155 ---
obs-22750 --
Displacement parametersBiso mean: 52.59 Å2
Baniso -1Baniso -2Baniso -3
1-6.0212 Å20 Å2-0.6766 Å2
2---11.7768 Å20 Å2
3---5.7556 Å2
Refine analyzeLuzzati coordinate error obs: 0.309 Å
Refinement stepCycle: LAST / Resolution: 2.14→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 45 135 3047
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: 2.14→2.19 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2632 154 5.59 %
Rwork0.23 2602 -

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