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- PDB-2zi7: C4S dCK variant of dCK in complex with D-dG+UDP -

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Basic information

Entry
Database: PDB / ID: 2zi7
TitleC4S dCK variant of dCK in complex with D-dG+UDP
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / dCK / purine / deoxyguanosine / deoxycytidine kinase / nucleoside / enantiomer / D-dG / dG / 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 / 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
2'-DEOXY-GUANOSINE / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSabini, E. / Lavie, A.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Elucidation of different binding modes of purine nucleosides to human deoxycytidine kinase
Authors: Sabini, E. / Hazra, S. / Konrad, M. / Lavie, A.
History
DepositionFeb 13, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 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_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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 1.3Nov 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
B: Deoxycytidine kinase
A: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4886
Polymers65,1452
Non-polymers1,3434
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-20.1 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.800, 107.500, 110.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Deoxycytidine kinase / dCK


Mass: 32572.510 Da / Num. of mol.: 2 / Mutation: C9S, C45S, C59S, C146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27707, deoxycytidine kinase
#2: Chemical ChemComp-GNG / 2'-DEOXY-GUANOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.99 Å3/Da / Density % sol: 38.34 %
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: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. all: 36226 / Num. obs: 36226 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.1
Reflection shellResolution: 1.97→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1316 / % possible all: 79.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SERGUIdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P5Z

1p5z


Resolution: 1.97→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.788 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.194 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25877 3607 10 %RANDOM
Rwork0.20606 ---
obs0.21127 32619 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.641 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2--1.99 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 88 84 3697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223704
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9745034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0315419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.64924.457184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12615630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0091519
X-RAY DIFFRACTIONr_chiral_restr0.1160.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022783
X-RAY DIFFRACTIONr_nbd_refined0.2050.21665
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22486
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.26
X-RAY DIFFRACTIONr_mcbond_it1.0551.52178
X-RAY DIFFRACTIONr_mcangle_it1.76223429
X-RAY DIFFRACTIONr_scbond_it2.55931812
X-RAY DIFFRACTIONr_scangle_it3.7394.51605
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 239 -
Rwork0.281 2127 -
obs--86.89 %

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