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- PDB-2zi6: C4S dCK variant of dCK in complex with D-dA+UDP -

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Basic information

Entry
Database: PDB / ID: 2zi6
TitleC4S dCK variant of dCK in complex with D-dA+UDP
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / dCK / purine / deoxyadenosine / deoxycytidine kinase / nucleoside / enantiomer / D-dA / UDP / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein
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 / cytoplasm / cytosol
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
Chem-3D1 / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSabini, E. / Lavie, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural basis for substrate promiscuity of dCK
Authors: Sabini, E. / Hazra, S. / Ort, S. / Konrad, M. / Lavie, A.
History
DepositionFeb 13, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)132,91212
Polymers130,2904
Non-polymers2,6228
Water2,972165
1
A: Deoxycytidine kinase
B: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2648
Polymers65,1452
Non-polymers2,1196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-18.3 kcal/mol
Surface area20220 Å2
MethodPISA
2
C: Deoxycytidine kinase
hetero molecules

C: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6484
Polymers65,1452
Non-polymers5022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4730 Å2
ΔGint-13.3 kcal/mol
Surface area19670 Å2
MethodPISA
3
D: Deoxycytidine kinase
hetero molecules

D: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6484
Polymers65,1452
Non-polymers5022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area4630 Å2
ΔGint-19 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.250, 138.510, 118.670
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


Mass: 32572.510 Da / Num. of mol.: 4 / Mutation: C9S, C45S, C59S, C146S
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-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-3D1 / (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol / 2'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0M Sodium Citrate, 100mM Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / Num. all: 109802 / Num. obs: 109802 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.4
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 4 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3 / Num. unique all: 16552 / % possible all: 93

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Processing

Software
NameClassification
SERGUIdata collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENRTY 1P5Z

1p5z


Resolution: 1.77→30 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection
Rfree0.2834 -
Rwork0.2077 -
all-98498
obs-98498
Refinement stepCycle: LAST / Resolution: 1.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7279 0 172 165 7616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.027

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