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

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Basic information

Entry
Database: PDB / ID: 2vqs
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
5-BROMOVINYLDEOXYURIDINE / Deoxynucleoside kinase
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionMar 18, 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)109,34412
Polymers107,6274
Non-polymers1,7178
Water88349
1
A: DEOXYNUCLEOSIDE KINASE
B: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6726
Polymers53,8132
Non-polymers8584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-37 kcal/mol
Surface area20290 Å2
MethodPQS
2
C: DEOXYNUCLEOSIDE KINASE
D: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6726
Polymers53,8132
Non-polymers8584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-31.8 kcal/mol
Surface area20250 Å2
MethodPQS
Unit cell
Length a, b, c (Å)137.644, 112.828, 69.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A12 - 160
2111B12 - 160
3111C12 - 160
4111D12 - 160
1211A175 - 208
2211B175 - 208
3211C175 - 208
4211D175 - 208

NCS oper: (Code: given
Matrix: (-0.95, 0.01154, 0.312), (-0.02146, -0.9994, -0.02838), (0.3115, -0.03366, 0.9497)
Vector: 33.81, -4.907, -5.535)

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-BVD / 5-BROMOVINYLDEOXYURIDINE


Mass: 333.135 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13BrN2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.08 Å3/Da / Density % sol: 51.08 % / 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: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 19428 / % possible obs: 83.5 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.5
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 87.2

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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: 2.9→30 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.865 / SU B: 19.985 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R Free: 0.511 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1031 5 %RANDOM
Rwork0.242 ---
obs0.244 19428 82.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å20 Å20 Å2
2---3.15 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6125 0 96 49 6270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226364
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9728608
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65624.521303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.663151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2421529
X-RAY DIFFRACTIONr_chiral_restr0.090.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024705
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.22945
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.24268
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5250.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6551.53757
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18225983
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.27433007
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9924.52625
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 1457 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
3Ctight positional0.050.05
4Dtight positional0.050.05
1Atight thermal0.10.5
2Btight thermal0.10.5
3Ctight thermal0.090.5
4Dtight thermal0.110.5
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.369 67
Rwork0.321 1477

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