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- PDB-1p61: Structure of human dCK complexed with 2'-Deoxycytidine and ADP, P... -

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Basic information

Entry
Database: PDB / ID: 1p61
TitleStructure of human dCK complexed with 2'-Deoxycytidine and ADP, P 43 21 2 space group
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / nucleoside kinase / P-loop / deoxycytidine
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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 2'-DEOXYCYTIDINE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å
AuthorsSabini, E. / Ort, S. / Monnerjahn, C. / Konrad, M. / Lavie, A.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structure of human dCK suggests strategies to improve anticancer and antiviral therapy
Authors: Sabini, E. / Ort, S. / Monnerjahn, C. / Konrad, M. / Lavie, A.
History
DepositionApr 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4893
Polymers30,8351
Non-polymers6542
Water2,360131
1
B: Deoxycytidine kinase
hetero molecules

B: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9786
Polymers61,6702
Non-polymers1,3094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4840 Å2
ΔGint-19 kcal/mol
Surface area19840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.001, 80.001, 93.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-424-

HOH

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Components

#1: Protein Deoxycytidine kinase / dCK


Mass: 30834.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27707, deoxycytidine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-DCZ / 2'-DEOXYCYTIDINE


Type: DNA OH 5 prime terminus / Mass: 227.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.95-1.0M citrate trisodium dihydrate, 100mM Hepes, 5mM deoxycytidine, 5mM ADP, 5mM MgCl2, 5mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlenzyme1drop
25 mM1dropMgCl2
320 mMHEPES1droppH7.5
45 mMdithiothreitol1drop
5100000 nMdeoxycytidine1drop
60.95-1.0 Mtrisodium citrate dihydrate1reservoir
7100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9552 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 21, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9552 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 15208 / Rsym value: 0.064 / Net I/σ(I): 28.2
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 7.5 / Rsym value: 0.156
Reflection
*PLUS
Num. obs: 15406 / % possible obs: 95.9 % / Num. measured all: 219344 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 78.2 % / Rmerge(I) obs: 0.156

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.21→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.278 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27964 1537 10.1 %RANDOM
Rwork0.22158 ---
obs0.22733 13671 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.706 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å20 Å2
2--2.17 Å20 Å2
3----4.34 Å2
Refinement stepCycle: LAST / Resolution: 2.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 43 131 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211961
X-RAY DIFFRACTIONr_bond_other_d0.0020.021713
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.9622668
X-RAY DIFFRACTIONr_angle_other_deg0.91533981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9425227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022159
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02414
X-RAY DIFFRACTIONr_nbd_refined0.2190.2422
X-RAY DIFFRACTIONr_nbd_other0.250.21948
X-RAY DIFFRACTIONr_nbtor_other0.0950.21151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3950.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0971.51141
X-RAY DIFFRACTIONr_mcangle_it221834
X-RAY DIFFRACTIONr_scbond_it2.6583820
X-RAY DIFFRACTIONr_scangle_it4.254.5834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.209→2.266 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.666 100
Rwork0.652 878
Refinement
*PLUS
Highest resolution: 2.2 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.885

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