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- PDB-2vp4: Structural Studies of Nucleoside Analog and Feedback Inhibitor Bi... -

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Basic information

Entry
Database: PDB / ID: 2vp4
TitleStructural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase
ComponentsDEOXYNUCLEOSIDE KINASE
KeywordsTRANSFERASE / ATP-BINDING / DNA SYNTHESIS / PHOSPHOPROTEIN / FEEDBACK INHIBITION / DEOXYRIBONUCLEOSIDE KINASE / SALVAGE PATHWAY / NUCLEOTIDE-BINDING / DTTP / KINASE / COMPLEX / DROSOPHILA
Function / homology
Function and homology information


deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / uridine kinase activity / nucleoside salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / thymidine kinase activity / deoxyadenosine kinase activity ...deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / uridine kinase activity / nucleoside salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / thymidine kinase activity / deoxyadenosine kinase activity / cytidine kinase activity / DNA biosynthetic process / kinase activity / mitochondrion / ATP binding / 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'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxynucleoside kinase
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMikkelsen, N.E. / Munch-Petersen, B. / Eklund, H.
CitationJournal: FEBS J. / Year: 2008
Title: Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase.
Authors: Mikkelsen, N.E. / Munch-Petersen, B. / Eklund, H.
History
DepositionFeb 26, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEOXYNUCLEOSIDE KINASE
B: DEOXYNUCLEOSIDE KINASE
C: DEOXYNUCLEOSIDE KINASE
D: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4958
Polymers107,6274
Non-polymers1,8694
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-58.5 kcal/mol
Surface area39990 Å2
MethodPQS
Unit cell
Length a, b, c (Å)67.858, 119.034, 70.511
Angle α, β, γ (deg.)90.00, 96.38, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.004896, 0.005218), (0.004766, -0.9997, -0.02464), (0.005337, -0.02461, 0.9997)
Vector: 59.63, 1.226, -0.1769)

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Components

#1: Protein
DEOXYNUCLEOSIDE KINASE / DEOXYRIBONUCLEOSIDE KINASE / DM-DNK / MULTISPECIFIC DEOXYNUCLEOSIDE KINASE


Mass: 26906.707 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9XZT6, deoxynucleoside kinase
#2: Chemical
ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.82 Å3/Da / Density % sol: 56.07 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.981661
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981661 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 53215 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J90

1j90


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.047 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2850 5.1 %RANDOM
Rwork0.195 ---
obs0.197 53215 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20.6 Å2
2---2.08 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6592 0 112 459 7163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226860
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9779296
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31423.964338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.304151258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261548
X-RAY DIFFRACTIONr_chiral_restr0.0940.2998
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025108
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.23250
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24568
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2506
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3550.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4130.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7241.54104
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20926440
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.81633211
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7394.52856
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 203
Rwork0.263 3917

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