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- PDB-3g15: Crystal structure of human choline kinase alpha in complex with h... -

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Basic information

Entry
Database: PDB / ID: 3g15
TitleCrystal structure of human choline kinase alpha in complex with hemicholinium-3 and ADP
ComponentsCholine kinase alpha
KeywordsTRANSFERASE / NON-PROTEIN KINASE / CHOLINE KINASE / STRUCTURAL GENOMICS Consortium / SGC / hemicholinium-3 / Kinase
Function / homology
Function and homology information


ethanolamine kinase / choline kinase / ethanolamine kinase activity / Synthesis of PE / choline kinase activity / CDP-choline pathway / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / Synthesis of PE / 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
ADENOSINE-5'-DIPHOSPHATE / Chem-HC6 / Choline kinase alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsHong, B.S. / Tempel, W. / Rabeh, W.M. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.W. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of human choline kinase isoforms in complex with hemicholinium-3: single amino acid near the active site influences inhibitor sensitivity.
Authors: Hong, B.S. / Allali-Hassani, A. / Tempel, W. / Finerty, P.J. / Mackenzie, F. / Dimov, S. / Vedadi, M. / Park, H.W.
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 10, 2009ID: 3F2S
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 21, 2020Group: Data collection / Database references / Derived calculations
Category: pdbx_struct_conn_angle / phasing ...pdbx_struct_conn_angle / phasing / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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
Revision 1.4Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Choline kinase alpha
B: Choline kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,68633
Polymers93,7132
Non-polymers1,97331
Water5,837324
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-109 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.802, 118.986, 131.039
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Choline kinase alpha / CK / CHETK-alpha


Mass: 46856.477 Da / Num. of mol.: 2 / Fragment: UNP residues 75-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHKA, CHK, CKI / Plasmid: pET28aLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P35790, choline kinase

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Non-polymers , 6 types, 355 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-HC6 / (2S,2'S)-2,2'-biphenyl-4,4'-diylbis(2-hydroxy-4,4-dimethylmorpholin-4-ium)


Mass: 414.538 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H34N2O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 21 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG-3350, 0.2M lithium sulfate, 0.1M HEPES. Crystallization sample buffer: 0.01M TRIS pH 8.0, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M DTT, 0.003M hemicholinium-3, 0.005M ...Details: 25% PEG-3350, 0.2M lithium sulfate, 0.1M HEPES. Crystallization sample buffer: 0.01M TRIS pH 8.0, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M DTT, 0.003M hemicholinium-3, 0.005M ADP., vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96863 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2008
RadiationProtocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 93657 / % possible obs: 97 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.069 / Χ2: 1.585 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.762.60.79771621.75275.6
1.76-1.8340.68690121.52294.3
1.83-1.915.90.56395331.42399.8
1.91-2.027.10.39495741.419100
2.02-2.147.40.25195811.501100
2.14-2.317.40.17396061.581100
2.31-2.547.50.11596471.538100
2.54-2.917.50.07596851.63100
2.91-3.667.40.04997542.025100
3.66-507.20.031101031.50499.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
Cootmodel building
MolProbitymodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I7Q

2i7q


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.213 / SU B: 2.363 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HEMICHOLINIUM-3 RESTRAINTS WERE PREPARED BY THE PRODRG SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2122 2.272 %thin shells (sftools)
Rwork0.22 ---
obs0.221 93409 96.694 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.163 Å2
Baniso -1Baniso -2Baniso -3
1--0.522 Å20 Å20 Å2
2--1.292 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5354 0 149 324 5827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225670
X-RAY DIFFRACTIONr_bond_other_d0.0020.023911
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9927696
X-RAY DIFFRACTIONr_angle_other_deg2.1893.0079476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4545669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11923.424257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75815961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0771531
X-RAY DIFFRACTIONr_chiral_restr0.0830.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021241
X-RAY DIFFRACTIONr_mcbond_it2.01223322
X-RAY DIFFRACTIONr_mcbond_other0.58621327
X-RAY DIFFRACTIONr_mcangle_it2.99235332
X-RAY DIFFRACTIONr_scbond_it2.4122348
X-RAY DIFFRACTIONr_scangle_it3.47932357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74400.3374998705070.894
1.744-1.79200.3136002684287.723
1.792-1.84400.2756453665596.965
1.844-1.90.2985680.2685919651899.524
1.9-1.96200.2356271628099.857
1.962-2.03100.2246100611199.82
2.031-2.10700.2155898590399.915
2.107-2.1930.2534800.2125181566999.859
2.193-2.2900.2125464546799.945
2.29-2.4010.3220.2125191521599.962
2.401-2.530.2553500.2134670502199.98
2.53-2.68200.2224700470799.851
2.682-2.8660.2722780.2234156443699.955
2.866-3.09300.2244178417999.976
3.093-3.3840.2541790.22636553834100
3.384-3.77800.2023495349699.971
3.778-4.3510.1981150.1722997311399.968
4.351-5.30100.18526682668100
5.301-7.3820.239780.25520522130100
7.382-300.344520.261239130998.625

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