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- PDB-3mes: Crystal structure of choline kinase from Cryptosporidium parvum I... -

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Basic information

Entry
Database: PDB / ID: 3mes
TitleCrystal structure of choline kinase from Cryptosporidium parvum Iowa II, cgd3_2030
ComponentsCholine kinase
KeywordsTRANSFERASE / choline kinase / malaria / Structural Genomics / Structural Genomics Consortium / SGC / Kinase
Function / homology
Function and homology information


ethanolamine kinase activity / choline kinase activity / phosphatidylethanolamine biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Choline/ethanolamine kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DECAMETHONIUM ION / N-PROPYL-TARTRAMIC ACID / Putative choline kinase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsQiu, W. / Wernimont, A. / Hills, T. / Lew, J. / Artz, J.D. / Xiao, T. / Allali-Hassani, A. / Vedadi, M. / Kozieradzki, I. / Cossar, D. ...Qiu, W. / Wernimont, A. / Hills, T. / Lew, J. / Artz, J.D. / Xiao, T. / Allali-Hassani, A. / Vedadi, M. / Kozieradzki, I. / Cossar, D. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Ma, D. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of choline kinase from Cryptosporidium parvum Iowa II, cgd3_2030
Authors: Qiu, W. / Wernimont, A. / Hills, T. / Lew, J. / Artz, J.D. / Xiao, T. / Allali-Hassani, A. / Vedadi, M. / Kozieradzki, I. / Cossar, D. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / ...Authors: Qiu, W. / Wernimont, A. / Hills, T. / Lew, J. / Artz, J.D. / Xiao, T. / Allali-Hassani, A. / Vedadi, M. / Kozieradzki, I. / Cossar, D. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Ma, D.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_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: Choline kinase
B: Choline kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,19513
Polymers99,2512
Non-polymers1,94311
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-50 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.091, 67.957, 92.109
Angle α, β, γ (deg.)90.00, 116.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Choline kinase / ethanolamine kinase


Mass: 49625.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd3_2030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CUP2

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Non-polymers , 6 types, 259 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DME / DECAMETHONIUM ION


Mass: 258.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H38N2
#5: Chemical ChemComp-PT3 / N-PROPYL-TARTRAMIC ACID


Mass: 191.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO5
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18.5% P3350, 0.2 M KNa-Tartrate, 2 mM Decamethonium bromide, 2 mM TCEP, 2 mM ADP and 4 mM MgCl2, 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: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 39440 / Num. obs: 39277 / % possible obs: 99.6 % / Redundancy: 3.68 % / Rsym value: 0.1382 / Net I/σ(I): 7.68
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 3.65 % / Mean I/σ(I) obs: 2.14 / Num. unique all: 4578 / Rsym value: 0.4979 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
BALBESphasing
REFMAC5.5.0066refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FI8

3fi8


Resolution: 2.35→19.72 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.852 / SU B: 9.748 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.43 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29108 1964 5 %RANDOM
Rwork0.24498 ---
obs0.24733 37308 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.144 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å21.56 Å2
2---1.7 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5952 0 126 248 6326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0226242
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6591.9748430
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.915709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9324.791311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.577151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0921526
X-RAY DIFFRACTIONr_chiral_restr0.0470.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214624
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2171.53589
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.425835
X-RAY DIFFRACTIONr_scbond_it0.37632653
X-RAY DIFFRACTIONr_scangle_it0.654.52595
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 143 -
Rwork0.302 2710 -
obs--100 %

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