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- PDB-3pm8: CAD domain of PFF0520w, Calcium dependent protein kinase -

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Basic information

Entry
Database: PDB / ID: 3pm8
TitleCAD domain of PFF0520w, Calcium dependent protein kinase
ComponentsCalcium-dependent protein kinase 2
KeywordsTRANSFERASE / malaria / structural genomics / cdpk / Structural Genomics Consortium / SGC / calcium binding domain - CDPK activation domain
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / calcium ion binding / ATP binding
Similarity search - Function
EF-hand / Recoverin; 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 / Serine/threonine-protein kinase, active site ...EF-hand / Recoverin; 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calcium-dependent protein kinase 2
Similarity search - Component
Biological speciesPlasmodium falciparum K1 (eukaryote)
MethodX-RAY DIFFRACTION / SAD/molecular replacement / Resolution: 2 Å
AuthorsWernimont, A.K. / Hutchinson, A. / Lew, J. / Chamberlain, K. / MacKenzie, F. / Loppnau, P. / Cossar, D. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. ...Wernimont, A.K. / Hutchinson, A. / Lew, J. / Chamberlain, K. / MacKenzie, F. / Loppnau, P. / Cossar, D. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: CAD domain of PFF0520w, Calcium dependent protein kinase
Authors: Wernimont, A.K. / Hutchinson, A. / Lew, J. / Chamberlain, K. / MacKenzie, F. / Loppnau, P. / Cossar, D. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Amani, M.
History
DepositionNov 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 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_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_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

Downloads & links

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Assembly

Deposited unit
A: Calcium-dependent protein kinase 2
B: Calcium-dependent protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,61413
Polymers45,2342
Non-polymers38011
Water2,072115
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-133 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.019, 51.378, 51.639
Angle α, β, γ (deg.)68.530, 65.750, 64.490
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is unknown as per authors

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Components

#1: Protein Calcium-dependent protein kinase 2 / PfCDPK2


Mass: 22616.900 Da / Num. of mol.: 2 / Fragment: UNP residues 335-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum K1 (eukaryote) / Gene: CPK2, CDPK2 / Plasmid: pet15 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21de3
References: UniProt: O15865, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2M MgCl2, 0.1M Hepes 7.5, 5mM CaCl2, 2.5mM MgCl2, glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 26094 / Num. obs: 24816 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.041 / Χ2: 1.716 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2-2.033.80.4843.4611631.68488.5
2.03-2.0740.3824.5112201.64393.1
2.07-2.1140.34611961.65792.9
2.11-2.1540.28412321.78493.1
2.15-2.240.23911791.70692.7
2.2-2.2540.2112481.74894.5
2.25-2.3140.17812321.74293.5
2.31-2.3740.15412101.66694.3
2.37-2.4440.12612591.75294.7
2.44-2.5240.11912271.70494.8
2.52-2.6140.10112551.75695.1
2.61-2.7140.0812271.69195.5
2.71-2.8440.06812731.71396.2
2.84-2.9940.05612301.71196.1
2.99-3.1740.04512681.65196.6
3.17-3.4240.03412781.66596.9
3.42-3.7640.02812631.58297.4
3.76-4.3140.02412871.54298
4.31-5.4340.02512731.65898.7
5.43-503.90.02412962.26398.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
PDB_EXTRACT3.1data extraction
PHASERphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD/molecular replacement
Starting model: 3l19

3l19


Resolution: 2→26.61 Å / Cor.coef. Fo:Fc: 0.9412 / Cor.coef. Fo:Fc free: 0.9292 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1268 5.11 %RANDOM
Rwork0.199 ---
all0.2004 26118 --
obs0.2004 24815 95.01 %-
Displacement parametersBiso max: 134.67 Å2 / Biso mean: 44.8422 Å2 / Biso min: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.8386 Å26.4529 Å22.555 Å2
2---0.3239 Å22.728 Å2
3---2.1625 Å2
Refine analyzeLuzzati coordinate error obs: 0.243 Å
Refinement stepCycle: LAST / Resolution: 2→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 11 115 2730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.08
X-RAY DIFFRACTIONt_bond_d0.01
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2662 145 5.07 %
Rwork0.2092 2713 -
all0.212 2858 -
obs-1730 -

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