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- PDB-3dfa: Crystal structure of kinase domain of calcium-dependent protein k... -

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Basic information

Entry
Database: PDB / ID: 3dfa
TitleCrystal structure of kinase domain of calcium-dependent protein kinase cgd3_920 from Cryptosporidium parvum
ComponentsCalcium-dependent protein kinase cgd3_920
KeywordsTRANSFERASE / calmodulin / kinase / malaria / 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 / 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
Calmodulin-domain protein kinase 1, putative
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsWernimont, A.K. / Lew, J. / Lin, Y.H. / Hassanali, A. / Khuu, C. / Alam, Z. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. ...Wernimont, A.K. / Lew, J. / Lin, Y.H. / Hassanali, A. / Khuu, C. / Alam, Z. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Wilkstrom, M. / Edwards, A.M. / Hui, R. / Artz, J.D. / Xiao, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of kinase domain of calcium-dependent protein kinase cgd3_920 from Cryptosporidium parvum.
Authors: Wernimont, A.K. / Lew, J. / Lin, Y.H. / Hassanali, A. / Khuu, C. / Alam, Z. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Wilkstrom, M. / Edwards, A.M. / ...Authors: Wernimont, A.K. / Lew, J. / Lin, Y.H. / Hassanali, A. / Khuu, C. / Alam, Z. / Kozieradzki, I. / Cossar, D. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Wilkstrom, M. / Edwards, A.M. / Hui, R. / Artz, J.D. / Xiao, T.
History
DepositionJun 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-dependent protein kinase cgd3_920


Theoretical massNumber of molelcules
Total (without water)33,3161
Polymers33,3161
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.447, 69.447, 137.414
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Calcium-dependent protein kinase cgd3_920


Mass: 33316.285 Da / Num. of mol.: 1 / Fragment: Kinase domain: Residues 70-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: CGD3_920 / Production host: Escherichia coli (E. coli) / References: UniProt: A3FQ16
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M Tris-HCl pH 7.6, 20% PEG 8000, 0.38 M Ammonium sulfate, 25% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.91996 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91996 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 12641 / Num. obs: 12641 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.064 / Χ2: 1.679 / Net I/σ(I): 11.2
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 4.53 / Num. unique all: 1058 / Rsym value: 0.411 / Χ2: 1.322 / % possible all: 83.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.71 Å
Translation2.5 Å34.71 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QG5

2qg5


Resolution: 2.45→49.09 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.932 / SU B: 20.505 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.481 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 611 4.9 %RANDOM
Rwork0.233 ---
all0.234 12590 --
obs0.234 12590 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.985 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å20 Å20 Å2
2---3.14 Å20 Å2
3---6.27 Å2
Refinement stepCycle: LAST / Resolution: 2.45→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 0 79 2183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222149
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.9572906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8485262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02124.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00115372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8331510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021605
X-RAY DIFFRACTIONr_nbd_refined0.180.2943
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21480
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.27
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.29
X-RAY DIFFRACTIONr_mcbond_it0.2051.51349
X-RAY DIFFRACTIONr_mcangle_it0.38222119
X-RAY DIFFRACTIONr_scbond_it0.5863910
X-RAY DIFFRACTIONr_scangle_it0.9264.5787
LS refinement shellResolution: 2.45→2.515 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 28 -
Rwork0.289 748 -
all-776 -
obs-1056 82.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.97915.94460.94193.24070.67710.2253-0.30952.665-1.3956-0.57840.67061.26570.84361.396-0.36110.76240.1672-0.02210.8771-0.18450.67623.729-15.13-21.577
25.0839-0.2930.52234.53090.98561.2834-0.06270.6176-0.5701-0.5301-0.0296-0.4550.07950.14970.09230.2440.0366-0.0240.12170.03370.27714.623-8.019-13.224
312.83557.76676.61817.6074.15376.094-0.2091.0279-0.1816-1.0338-0.02130.18580.03150.87920.23020.27920.0068-0.03560.17020.10540.24979.758-6.303-12.886
47.4928-3.72920.64417.2797-0.63072.45120.11650.24480.1216-0.6661-0.04-0.33520.27860.4278-0.07650.0401-0.04850.0550.20010.07060.117122.366-10.2090.953
52.43641.82892.96842.99860.12586.33580.1823-0.1524-1.5609-0.5120.139-0.17950.36210.2627-0.32130.1350.0359-0.04970.20350.10580.510411.154-14.121-1.056
66.2968-0.9187-0.3843.7103-0.23693.127-0.0968-0.4773-0.4032-0.00810.15310.19120.20410.0728-0.0563-0.0917-0.0037-0.02260.13680.10810.136114.774-14.13712.59
78.1926-2.070.40135.19760.03853.0592-0.1634-0.74190.31940.28190.1716-0.6982-0.23090.4177-0.0082-0.0507-0.0285-0.08320.256-0.02340.222325.271-7.81115.667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 1715 - 34
2X-RAY DIFFRACTION2AA18 - 5935 - 76
3X-RAY DIFFRACTION3AA60 - 8677 - 103
4X-RAY DIFFRACTION4AA87 - 137104 - 154
5X-RAY DIFFRACTION5AA142 - 170159 - 187
6X-RAY DIFFRACTION6AA171 - 215188 - 232
7X-RAY DIFFRACTION7AA216 - 267233 - 284

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