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- PDB-1ot3: Crystal structure of Drosophila deoxyribonucleotide kinase comple... -

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Basic information

Entry
Database: PDB / ID: 1ot3
TitleCrystal structure of Drosophila deoxyribonucleotide kinase complexed with the substrate deoxythymidine
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
THYMIDINE / Deoxynucleoside kinase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMikkelsen, N.E. / Johansson, K. / Karlsson, A. / Knecht, W. / Andersen, G. / Piskur, J. / Munch-Petersen, B. / Eklund, H.
CitationJournal: Biochemistry / Year: 2003
Title: Structural Basis for Feedback Inhibition of the Deoxyribonucleoside Salvage Pathway: Studies of the Drosophila Deoxyribonucleoside Kinase.
Authors: Mikkelsen, N.E. / Johansson, K. / Karlsson, A. / Knecht, W. / Andersen, G. / Piskur, J. / Munch-Petersen, B. / Eklund, H.
History
DepositionMar 21, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 28, 2014Group: Other
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyribonucleoside Kinase
B: Deoxyribonucleoside Kinase
C: Deoxyribonucleoside Kinase
D: Deoxyribonucleoside Kinase
E: Deoxyribonucleoside Kinase
F: Deoxyribonucleoside Kinase
G: Deoxyribonucleoside Kinase
H: Deoxyribonucleoside Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,82025
Polymers233,0188
Non-polymers2,80217
Water5,585310
1
A: Deoxyribonucleoside Kinase
B: Deoxyribonucleoside Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0277
Polymers58,2552
Non-polymers7735
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-57 kcal/mol
Surface area17800 Å2
MethodPISA
2
C: Deoxyribonucleoside Kinase
D: Deoxyribonucleoside Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9316
Polymers58,2552
Non-polymers6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-58 kcal/mol
Surface area17430 Å2
MethodPISA
3
E: Deoxyribonucleoside Kinase
F: Deoxyribonucleoside Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9316
Polymers58,2552
Non-polymers6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-59 kcal/mol
Surface area17410 Å2
MethodPISA
4
G: Deoxyribonucleoside Kinase
H: Deoxyribonucleoside Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9316
Polymers58,2552
Non-polymers6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-68 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.379, 71.158, 226.272
Angle α, β, γ (deg.)90.00, 90.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Deoxyribonucleoside Kinase / Dm-dNK


Mass: 29127.254 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9XZT6, deoxynucleoside kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE / Thymidine


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N2O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.03 Å3/Da / Density % sol: 59.14 %
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
Temperature: 14 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MMES1reservoirpH6.5
20.2 Mammonium sulfate1reservoir
318-22 %(w/v)MPEG50001reservoir
45-10 %(w/v)PEG4001reservoir
55-10 mg/mlprotein1drop
65 mMdT1dropor dTTP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93927 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2002
RadiationMonochromator: DIAMOND CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 77914 / Num. obs: 70001 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 54.664 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.05 / Net I/σ(I): 8
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 1.8 / Num. unique all: 7680 / Rsym value: 0.236 / % possible all: 68.1
Reflection
*PLUS
Lowest resolution: 70 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Lowest resolution: 2.64 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.236

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J90

1j90


Resolution: 2.5→25 Å / σ(F): 1.8 / σ(I): 1.8 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 3560 -RANDOM
Rwork0.227 ---
all-77914 --
obs-70001 89.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.087 Å20 Å214.047 Å2
2---9.358 Å20 Å2
3---12.445 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12847 0 181 310 13338
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4921.5
X-RAY DIFFRACTIONc_mcangle_it2.5752
X-RAY DIFFRACTIONc_scbond_it1.9412
X-RAY DIFFRACTIONc_scangle_it2.9732.5
LS refinement shellResolution: 2.5→2.61 Å
RfactorNum. reflection
Rfree0.3843 304
Rwork0.3184 -
obs-6107
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5thm_xplor_paramthm_xplor_top
Refinement
*PLUS
Lowest resolution: 70 Å / Rfactor Rfree: 0.276
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d0.994

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