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- PDB-2ckq: Crystal structure of Human Choline Kinase alpha 2 in complex with... -

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Basic information

Entry
Database: PDB / ID: 2ckq
TitleCrystal structure of Human Choline Kinase alpha 2 in complex with Phosphocholine
ComponentsCHOLINE KINASE ALPHA
KeywordsTRANSFERASE / PHOSPHATIDYLCHOLINE / PHOSPHOLIPID SYNTHESIS
Function / homology
Function and homology information


ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / 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 / phosphorylation / protein homodimerization activity / ATP binding / cytoplasm / cytosol
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
PHOSPHOCHOLINE / Choline kinase alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Nov 14, 2012Group: Database references / Other
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)91,1214
Polymers90,7532
Non-polymers3682
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint3.3 kcal/mol
Surface area31130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.500, 128.300, 172.200
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 / ETHANOLAMINE KINASE / EK


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, ethanolamine kinase
#2: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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 SEQUENCE FROM OUR CONSTRUCT LACKS THE FIRST N-TERMINAL 49 RESIDUES. THE SEQUENCE BELOW CORRESPONDS TO ISOFORM 2 OF CHOLINE KINASE (MISSING 155-172) MET 154 TO VAL 154 OBSERVED IN EMBL-CDS:BAA01547.

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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: 3.64 Å3/Da / Density % sol: 65.9 %
Crystal growpH: 7.5 / Details: 0.01 M MGCL2, 15% PEG 3350, 0.2 M NAF., pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 46369 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.9
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NW1

1nw1


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 17.554 / SU ML: 0.198 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 4638 10 %RANDOM
Rwork0.214 ---
obs0.219 41524 99.9 %-
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: 35.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2---2.86 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5534 0 22 109 5665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225747
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.967778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53622.917264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95515949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3311537
X-RAY DIFFRACTIONr_chiral_restr0.0850.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024376
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.22505
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23936
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5681.53575
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97425526
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.22632513
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0144.52250
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.37 329
Rwork0.29 2889
Refinement TLS params.Method: refined / Origin x: 7.829 Å / Origin y: -16.2316 Å / Origin z: -33.0799 Å
111213212223313233
T-0.1105 Å2-0.0154 Å20.0203 Å2--0.0327 Å20.0204 Å2---0.0348 Å2
L0.215 °2-0.491 °20.2364 °2-1.2265 °2-0.5832 °2--0.7167 °2
S0.0029 Å °0.0563 Å °0.1095 Å °-0.0036 Å °-0.0088 Å °-0.0624 Å °-0.0482 Å °0.0331 Å °0.0058 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A85 - 457
2X-RAY DIFFRACTION1B82 - 457

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