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- PDB-1j90: Crystal Structure of Drosophila Deoxyribonucleoside Kinase -

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Basic information

Entry
Database: PDB / ID: 1j90
TitleCrystal Structure of Drosophila Deoxyribonucleoside Kinase
ComponentsDeoxyribonucleoside kinase
KeywordsTRANSFERASE / Protein-deoxynucleoside complex
Function / homology
Function and homology information


deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / nucleoside salvage / uridine kinase activity / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / thymidine kinase activity / deoxyguanosine kinase activity / deoxyadenosine kinase activity ...deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / nucleoside salvage / uridine kinase activity / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / thymidine kinase activity / deoxyguanosine kinase activity / deoxyadenosine kinase activity / cytidine kinase activity / DNA biosynthetic process / kinase activity / phosphorylation / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Deoxynucleoside kinase / Deoxynucleoside kinase domain / Deoxynucleoside kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE / Deoxynucleoside kinase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.56 Å
AuthorsJohansson, K. / Ramaswamy, S. / Ljungkrantz, C. / Knecht, W. / Piskur, J. / Munch-Petersen, B. / Eriksson, S. / Eklund, H.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structural basis for substrate specificities of cellular deoxyribonucleoside kinases.
Authors: Johansson, K. / Ramaswamy, S. / Ljungcrantz, C. / Knecht, W. / Piskur, J. / Munch-Petersen, B. / Eriksson, S. / Eklund, H.
History
DepositionMay 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE LAST 20 RESIDUES OF THE SEQUENCE DATABASE REFERENCE, RESIDUES 231-250, WERE TRUNCATED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyribonucleoside kinase
B: Deoxyribonucleoside kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4606
Polymers53,8132
Non-polymers6474
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-53 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.456, 60.749, 67.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological dimer is present in the asymmetric unit

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Components

#1: Protein Deoxyribonucleoside kinase


Mass: 26906.707 Da / Num. of mol.: 2 / Fragment: Truncation mutant / Mutation: Deletion of last 20 residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XZT6
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DCZ / 2'-DEOXYCYTIDINE / Deoxycytidine


Type: DNA OH 5 prime terminus / Mass: 227.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, mPEG5000, PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MMES1reservoirpH6.5
20.2 Mammonium sulfate1reservoir
320 %(w/v)PEG50001reservoir
48-10 %(v/v)PEG4001reservoir
510 mg/mlprotein1drop
610 mMdeoxycytidine1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 30, 2000
RadiationMonochromator: diamond crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.56→30 Å / Num. all: 17611 / Num. obs: 17594 / % possible obs: 99.9 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2 / Redundancy: 4.6 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.5
Reflection shellResolution: 2.56→2.72 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 25 Å
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.56 Å / % possible obs: 99.9 %

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Processing

Software
NameClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.56→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 785 -RANDOM
Rwork0.238 ---
obs0.26 16081 98.2 %-
all-16081 --
Displacement parametersBiso mean: 43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 42 141 3404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_d1.15
LS refinement shellResolution: 2.56→2.72 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.29 125 -
Rwork0.274 --
obs-2289 90.1 %
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor all: 0.26 / Rfactor obs: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.26
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.56 Å

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