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- PDB-2vp9: Structural Studies of Nucleoside Analog and Feedback Inhibitor Bi... -

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Basic information

Entry
Database: PDB / ID: 2vp9
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',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE / 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
DepositionFeb 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
E: DEOXYNUCLEOSIDE KINASE
F: DEOXYNUCLEOSIDE KINASE
G: DEOXYNUCLEOSIDE KINASE
H: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,44825
Polymers215,2548
Non-polymers3,19417
Water1,928107
1
A: DEOXYNUCLEOSIDE KINASE
B: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6847
Polymers53,8132
Non-polymers8715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-28.3 kcal/mol
Surface area22020 Å2
MethodPQS
2
C: DEOXYNUCLEOSIDE KINASE
D: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5886
Polymers53,8132
Non-polymers7754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-27.9 kcal/mol
Surface area21810 Å2
MethodPQS
3
E: DEOXYNUCLEOSIDE KINASE
F: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5886
Polymers53,8132
Non-polymers7754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-31.1 kcal/mol
Surface area21750 Å2
MethodPQS
4
G: DEOXYNUCLEOSIDE KINASE
H: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5886
Polymers53,8132
Non-polymers7754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-35 kcal/mol
Surface area21520 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.500, 70.820, 226.032
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRSERSERAA12 - 14212 - 142
21THRTHRSERSERBB12 - 14212 - 142
31THRTHRSERSERCC12 - 14212 - 142
41THRTHRSERSERDD12 - 14212 - 142
51THRTHRSERSEREE12 - 14212 - 142
61THRTHRSERSERFF12 - 14212 - 142
71THRTHRSERSERGG12 - 14212 - 142
81THRTHRSERSERHH12 - 14212 - 142
12GLNGLNALAALAAA146 - 160146 - 160
22GLNGLNALAALABB146 - 160146 - 160
32GLNGLNALAALACC146 - 160146 - 160
42GLNGLNALAALADD146 - 160146 - 160
52GLNGLNALAALAEE146 - 160146 - 160
62GLNGLNALAALAFF146 - 160146 - 160
72GLNGLNALAALAGG146 - 160146 - 160
82GLNGLNALAALAHH146 - 160146 - 160
13PROPROTRPTRPAA176 - 190176 - 190
23PROPROTRPTRPBB176 - 190176 - 190
33PROPROTRPTRPCC176 - 190176 - 190
43PROPROTRPTRPDD176 - 190176 - 190
53PROPROTRPTRPEE176 - 190176 - 190
63PROPROTRPTRPFF176 - 190176 - 190
73PROPROTRPTRPGG176 - 190176 - 190
83PROPROTRPTRPHH176 - 190176 - 190
14LYSLYSALAALAAA201 - 207201 - 207
24LYSLYSALAALABB201 - 207201 - 207
34LYSLYSALAALACC201 - 207201 - 207
44LYSLYSALAALADD201 - 207201 - 207
54LYSLYSALAALAEE201 - 207201 - 207
64LYSLYSALAALAFF201 - 207201 - 207
74LYSLYSALAALAGG201 - 207201 - 207
84LYSLYSALAALAHH201 - 207201 - 207

NCS oper: (Code: given
Matrix: (0.9767, -0.1546, -0.1487), (-0.1551, -0.9879, 0.008452), (-0.1482, 0.0148, -0.9889)
Vector: 3.907, 2.575, 47.34)

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Components

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


Mass: 26906.707 Da / Num. of mol.: 8 / 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.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-DOC / 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 291.198 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H14N3O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.07 Å3/Da / Density % sol: 53.06 % / 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: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 50991 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 97.1

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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: 0.89 / Cor.coef. Fo:Fc free: 0.863 / SU B: 18.405 / SU ML: 0.355 / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2468 5.1 %RANDOM
Rwork0.248 ---
obs0.25 45938 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å20 Å2-1.37 Å2
2--3.03 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12847 0 165 107 13119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02213303
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.96917984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9151531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28324.119653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.509152448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1181584
X-RAY DIFFRACTIONr_chiral_restr0.0960.21945
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029908
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.25869
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.28924
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2431
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3480.295
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6511.57830
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.195212532
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.32736226
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2124.55452
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: 1392 / 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 positional0.060.05
5Etight positional0.050.05
6Ftight positional0.050.05
7Gtight positional0.050.05
8Htight positional0.060.05
1Atight thermal0.130.5
2Btight thermal0.090.5
3Ctight thermal0.10.5
4Dtight thermal0.120.5
5Etight thermal0.10.5
6Ftight thermal0.120.5
7Gtight thermal0.10.5
8Htight thermal0.150.5
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.397 166
Rwork0.308 3362

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