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- PDB-2jj8: Structural Studies of Nucleoside Analog and Feedback Inhibitor Bi... -

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Basic information

Entry
Database: PDB / ID: 2jj8
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 / SALVAGE PATHWAY / NUCLEOTIDE-BINDING / DTTP
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
3'-azido-3'-deoxythymidine / Deoxynucleoside kinase
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _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: DEOXYNUCLEOSIDE KINASE
B: DEOXYNUCLEOSIDE KINASE
C: DEOXYNUCLEOSIDE KINASE
D: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,46416
Polymers107,6274
Non-polymers1,83712
Water1,00956
1
A: DEOXYNUCLEOSIDE KINASE
B: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7328
Polymers53,8132
Non-polymers9196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-103.8 kcal/mol
Surface area16930 Å2
MethodPISA
2
C: DEOXYNUCLEOSIDE KINASE
D: DEOXYNUCLEOSIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7328
Polymers53,8132
Non-polymers9196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-102 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.031, 111.868, 71.100
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:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 1 / Auth seq-ID: 12 - 208 / Label seq-ID: 12 - 208

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper: (Code: given
Matrix: (-0.9411, -0.01048, 0.338), (-0.008932, -0.9984, -0.05584), (0.338, -0.05557, 0.9395)
Vector: 33.57, -6.86, -6.112)

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Components

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


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.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-AZZ / 3'-azido-3'-deoxythymidine / Azidothymidine / Zidovudine


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.2 Å3/Da / Density % sol: 61.25 % / 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: Jul 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 26596 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8

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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: 2.8→20 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.867 / Cross valid method: THROUGHOUT / ESU R: 1.271 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1411 5 %RANDOM
Rwork0.235 ---
obs0.237 26596 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2---2.3 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6045 0 116 56 6217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226294
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9758518
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2875724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48924.49294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.538151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4871529
X-RAY DIFFRACTIONr_chiral_restr0.0840.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024641
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22788
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24274
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4550.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6081.53669
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15625939
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47332625
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4074.52579
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: 1427 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
3Ctight positional0.040.05
4Dtight positional0.040.05
1Atight thermal0.090.5
2Btight thermal0.10.5
3Ctight thermal0.090.5
4Dtight thermal0.090.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 87
Rwork0.298 1900

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