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- PDB-8ooj: Crystal structure of dCK C4S-S74E mutant in complex with EdC and UDP -

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Basic information

Entry
Database: PDB / ID: 8ooj
TitleCrystal structure of dCK C4S-S74E mutant in complex with EdC and UDP
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / Nucleoside kinase / phosphorylation / complex
Function / homology
Function and homology information


deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity ...deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity / pyrimidine nucleotide metabolic process / Purine salvage / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Deoxynucleoside kinase / : / Deoxynucleoside kinase domain / Deoxynucleoside kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Chem-VVC / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSaez-Ayala, M. / Rebuffet, E. / Betzi, S. / Morelli, X.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-INSB-05-01 France
CitationJournal: Mol.Cancer Ther. / Year: 2024
Title: 4'-Ethynyl-2'-Deoxycytidine (EdC) Preferentially Targets Lymphoma and Leukemia Subtypes by Inducing Replicative Stress.
Authors: Calbert, M.L. / Chandramouly, G. / Adams, C.M. / Saez-Ayala, M. / Kent, T. / Tyagi, M. / Ayyadevara, V.S.S.A. / Wang, Y. / Krais, J.J. / Gordon, J. / Atkins, J. / Toma, M.M. / Betzi, S. / ...Authors: Calbert, M.L. / Chandramouly, G. / Adams, C.M. / Saez-Ayala, M. / Kent, T. / Tyagi, M. / Ayyadevara, V.S.S.A. / Wang, Y. / Krais, J.J. / Gordon, J. / Atkins, J. / Toma, M.M. / Betzi, S. / Boghossian, A.S. / Rees, M.G. / Ronan, M.M. / Roth, J.A. / Goldman, A.R. / Gorman, N. / Mitra, R. / Childers, W.E. / Grana, X. / Skorski, T. / Johnson, N. / Hurtz, C. / Morelli, X. / Eischen, C.M. / Pomerantz, R.T.
History
DepositionApr 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxycytidine kinase
B: Deoxycytidine kinase
C: Deoxycytidine kinase
D: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,42812
Polymers130,8074
Non-polymers2,6228
Water93752
1
A: Deoxycytidine kinase
B: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7146
Polymers65,4032
Non-polymers1,3114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-29 kcal/mol
Surface area20660 Å2
MethodPISA
2
C: Deoxycytidine kinase
hetero molecules

C: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7146
Polymers65,4032
Non-polymers1,3114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3820 Å2
ΔGint-28 kcal/mol
Surface area21010 Å2
MethodPISA
3
D: Deoxycytidine kinase
hetero molecules

D: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7146
Polymers65,4032
Non-polymers1,3114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3800 Å2
ΔGint-30 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.470, 138.389, 116.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Deoxycytidine kinase / dCK / Deoxyadenosine kinase / Deoxyguanosine kinase


Mass: 32701.627 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Production host: Bacteria (eubacteria) / Strain (production host): BL21
References: UniProt: P27707, deoxycytidine kinase, 2'-deoxyadenosine kinase, deoxyguanosine kinase
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical
ChemComp-VVC / 4-azanyl-1-[(2~{R},4~{S},5~{R})-5-ethynyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one


Mass: 251.239 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES 70 mM pH 7.5 Sodium citrate 1.1 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.1→48.76 Å / Num. obs: 65390 / % possible obs: 99.8 % / Redundancy: 14.99 % / CC1/2: 0.999 / Net I/σ(I): 9.64
Reflection shellResolution: 2.1→2.22 Å / Num. unique obs: 10404 / CC1/2: 0.683

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.587 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27943 3255 5 %RANDOM
Rwork0.23667 ---
obs0.2388 61833 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.444 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0 Å20 Å2
2---3.43 Å2-0 Å2
3---4.78 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 0 172 52 7992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0128164
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167512
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.65311084
X-RAY DIFFRACTIONr_angle_other_deg0.3251.57217336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.925544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.051101460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0460.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029304
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021940
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_it2.625.3513720
X-RAY DIFFRACTIONr_mcbond_other2.6195.3513720
X-RAY DIFFRACTIONr_mcangle_it4.2159.6074640
X-RAY DIFFRACTIONr_mcangle_other4.2159.6084641
X-RAY DIFFRACTIONr_scbond_it2.8575.6164444
X-RAY DIFFRACTIONr_scbond_other2.8575.6164445
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.74410.1826437
X-RAY DIFFRACTIONr_long_range_B_refined7.27752.649409
X-RAY DIFFRACTIONr_long_range_B_other7.27852.649407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 238 -
Rwork0.421 4527 -
obs--99.98 %

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