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- PDB-2qg5: Cryptosporidium parvum calcium dependent protein kinase cgd7_1840 -

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Basic information

Entry
Database: PDB / ID: 2qg5
TitleCryptosporidium parvum calcium dependent protein kinase cgd7_1840
ComponentsCalcium/calmodulin-dependent protein kinase
KeywordsTRANSFERASE / malaria / calcium dependent kinase / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


starch binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding
Similarity search - Function
Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / 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. ...Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / 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. / Immunoglobulin-like fold / 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
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLunin, V.V. / Wernimont, A.K. / Lew, J. / Wasney, G. / Kozieradzki, I. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. ...Lunin, V.V. / Wernimont, A.K. / Lew, J. / Wasney, G. / Kozieradzki, I. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.E. / Hui, R. / Artz, J. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Cryptosporidium parvum calcium dependent protein kinase cgd7_1840
Authors: Lunin, V.V. / Wernimont, A.K. / Lew, J. / Wasney, G. / Kozieradzki, I. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.E. / Hui, R. / Artz, J. / Amani, M.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ...BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ACCORDING TO THE AUTHORS THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent protein kinase
B: Calcium/calmodulin-dependent protein kinase
D: Calcium/calmodulin-dependent protein kinase


Theoretical massNumber of molelcules
Total (without water)102,2703
Polymers102,2703
Non-polymers00
Water3,441191
1
A: Calcium/calmodulin-dependent protein kinase


Theoretical massNumber of molelcules
Total (without water)34,0901
Polymers34,0901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcium/calmodulin-dependent protein kinase


Theoretical massNumber of molelcules
Total (without water)34,0901
Polymers34,0901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Calcium/calmodulin-dependent protein kinase


Theoretical massNumber of molelcules
Total (without water)34,0901
Polymers34,0901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.178, 86.476, 87.965
Angle α, β, γ (deg.)90.00, 96.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase


Mass: 34090.035 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Plasmid: p15-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: Q5CYL9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.5M Na formate, 0.2M Bis Tris propane pH7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 38421 / Num. obs: 38421 / % possible obs: 88.39 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2732 / Rsym value: 0.455 / % possible all: 60.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YRP

1yrp


Resolution: 2.3→38.87 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.88 / SU B: 10.286 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.468 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28588 2104 5.2 %RANDOM
Rwork0.22012 ---
all0.22356 38421 --
obs0.22356 38421 88.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.035 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20.36 Å2
2---0.53 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6926 0 0 191 7117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227225
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.969779
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51323.209349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.8115.0351297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8421556
X-RAY DIFFRACTIONr_chiral_restr0.0990.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025508
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.22901
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24797
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2761.54439
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52626995
X-RAY DIFFRACTIONr_scbond_it2.68633178
X-RAY DIFFRACTIONr_scangle_it3.9124.52784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 72 -
Rwork0.288 1486 -
obs--46.67 %

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