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- PDB-2cko: Crystal structure of Human Choline Kinase alpha 2 -

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Basic information

Entry
Database: PDB / ID: 2cko
TitleCrystal structure of Human Choline Kinase alpha 2
ComponentsCHOLINE KINASE ALPHA
KeywordsTRANSFERASE / KINASE / CHOLINE KINASE / PHOSPHATYDILCHOLINE / ALTERNATIVE SPLICING
Function / homology
Function and homology information


ethanolamine kinase / choline kinase / Synthesis of PE / ethanolamine kinase activity / choline kinase activity / CDP-choline pathway / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / Synthesis of PE / ethanolamine kinase activity / choline kinase activity / CDP-choline pathway / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity / lipid transport / Synthesis of PC / cellular response to glucose starvation / lipid droplet / lipid metabolic process / protein tyrosine kinase activity / protein homodimerization activity / ATP binding / cytosol / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Choline kinase alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMalito, E. / Lavie, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Elucidation of Human Choline Kinase Crystal Structures in Complex with the Products Adp or Phosphocholine.
Authors: Malito, E. / Sekulic, N. / Too, W.C. / Konrad, M. / Lavie, A.
History
DepositionApr 20, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: CHOLINE KINASE ALPHA
B: CHOLINE KINASE ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0614
Polymers90,7532
Non-polymers3092
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.180, 122.820, 132.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHOLINE KINASE ALPHA / CK / CHETK-ALPHA


Mass: 45376.262 Da / Num. of mol.: 2 / Fragment: SPLICE ISOFORM 2, RESIDUES 50-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35790, choline kinase
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DESCRIBES THE HUMAN CHOLINE KINASE ISOFORM ALFA-2, ACCORDING TO AYOAMA ET AL., 2000. ...THE SEQUENCE DESCRIBES THE HUMAN CHOLINE KINASE ISOFORM ALFA-2, ACCORDING TO AYOAMA ET AL., 2000. THE UNIPROT DATABASE DESCRIBES IT AS ALFA-1. MOREOVER, THE SEQUENCE FROM OUR CONSTRUCT LACKS THE FIRST N-TER 49 RESIDUES. THE SEQUENCE BELOW CORRESPONDS TO ISOFORM 2 OF CHOLINE KINASE (FTID: VSP_009683)

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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: 2.66 Å3/Da / Density % sol: 53.42 %
Crystal growpH: 7.5 / Details: 0.01 M MGCL2, 15% PEG 3350, 0.2M NAF, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 50560 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 17.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 20.38
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 17.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 5.76 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NW1

1nw1


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.237 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.256 5080 10 %RANDOM
Rwork0.199 ---
obs0.204 45480 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2--2.01 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5686 0 16 417 6119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225847
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9677872
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36623.074283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.103151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4641543
X-RAY DIFFRACTIONr_chiral_restr0.0970.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024427
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22387
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23992
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2334
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8851.53583
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41825521
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06632654
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0774.52351
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 355
Rwork0.213 3273

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