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- PDB-1nw1: Crystal Structure of Choline Kinase -

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Basic information

Entry
Database: PDB / ID: 1nw1
TitleCrystal Structure of Choline Kinase
ComponentsCholine kinase (49.2 kD)
KeywordsTRANSFERASE / choline kinase / phospholipid synthesis / protein kinase fold
Function / homology
Function and homology information


Synthesis of PC / Synthesis of PE / ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / phosphatidylethanolamine biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Choline/Ethanolamine kinase / 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
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.02 Å
AuthorsPeisach, D. / Gee, P. / Kent, C. / Xu, Z.
CitationJournal: Structure / Year: 2003
Title: The Crystal Structure of Choline Kinase Reveals a Eukaryotic Protein Kinase Fold
Authors: Peisach, D. / Gee, P. / Kent, C. / Xu, Z.
History
DepositionFeb 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 30, 2014Group: Data collection
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_conn.ptnr2_label_seq_id / _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 (49.2 kD)
B: Choline kinase (49.2 kD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6824
Polymers98,6022
Non-polymers802
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-15 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.372, 102.141, 85.369
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Choline kinase (49.2 kD)


Mass: 49300.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pET43a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) cells / References: UniProt: Q22942, choline kinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.8 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 2000, calcium acetate, bicine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlcholine kinase1drop
220 mMbicine1droppH8.0
31 mMEGTA1drop
42 mMbeta-mercaptoethanol1drop
52 Mnondetergent sulfobetaine2011drop
68-10 %PEG20001reservoir
7200 mMcalcium acetate1reservoir
8100 mMbicine1reservoirpH8.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.0023 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 30, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0023 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 60790 / Num. obs: 58946 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.064 / Net I/σ(I): 14
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 6063 / Rsym value: 0.302 / % possible all: 99.8
Reflection
*PLUS
Num. obs: 60790 / % possible obs: 99.1 % / Num. measured all: 195184 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.02→37.54 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4367 7.4 %RANDOM
Rwork0.209 ---
obs0.209 58946 94.4 %-
all-60790 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.103 Å2 / ksol: 0.38892 e/Å3
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.02→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5809 0 2 342 6153
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 140 1.9 %
Rwork0.248 7091 -
obs-7231 67.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 37.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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