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- PDB-1zm7: Crystal structure of D. melanogaster deoxyribonucleoside kinase m... -

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Basic information

Entry
Database: PDB / ID: 1zm7
TitleCrystal structure of D. melanogaster deoxyribonucleoside kinase mutant N64D in complex with dTTP
ComponentsDeoxynucleoside kinase
KeywordsTRANSFERASE / Drosohila melanogaster / dnk / N64D / mutant
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-5'-TRIPHOSPHATE / Deoxynucleoside kinase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWelin, M. / Skovgaard, T. / Knecht, W. / Berenstein, D. / Munch-Petersen, B. / Piskur, J. / Eklund, H.
CitationJournal: Febs J. / Year: 2005
Title: Structural basis for the changed substrate specificity of Drosophila melanogaster deoxyribonucleoside kinase mutant N64D.
Authors: Welin, M. / Skovgaard, T. / Knecht, W. / Zhu, C. / Berenstein, D. / Munch-Petersen, B. / Piskur, J. / Eklund, H.
History
DepositionMay 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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)109,5849
Polymers107,6314
Non-polymers1,9535
Water3,495194
1
A: Deoxynucleoside kinase
B: Deoxynucleoside kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7804
Polymers53,8152
Non-polymers9642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-29 kcal/mol
Surface area17310 Å2
MethodPISA
2
C: Deoxynucleoside kinase
D: Deoxynucleoside kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8045
Polymers53,8152
Non-polymers9893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-39 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.040, 119.270, 68.388
Angle α, β, γ (deg.)90.00, 92.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR1AA12 - 5112 - 51
21THRTHRTHRTHR1BB12 - 5112 - 51
31THRTHRTHRTHR1CC12 - 5112 - 51
41THRTHRTHRTHR1DD12 - 5112 - 51
52PROPROTYRTYR1AA53 - 16153 - 161
62PROPROTYRTYR1BB53 - 16153 - 161
72PROPROTYRTYR1CC53 - 16153 - 161
82PROPROTYRTYR1DD53 - 16153 - 161
93ARGARGILEILE1AA163 - 164163 - 164
103ARGARGILEILE1BB163 - 164163 - 164
113ARGARGILEILE1CC163 - 164163 - 164
123ARGARGILEILE1DD163 - 164163 - 164
134ARGARGLEULEU1AA167 - 191167 - 191
144ARGARGLEULEU1BB167 - 191167 - 191
154ARGARGLEULEU1CC167 - 191167 - 191
164ARGARGLEULEU1DD167 - 191167 - 191
175ILEILECYSCYS2AA192 - 200192 - 200
185ILEILECYSCYS2BB192 - 200192 - 200
195ILEILECYSCYS2CC192 - 200192 - 200
205ILEILECYSCYS2DD192 - 200192 - 200
216LYSLYSASPASP1AA201 - 208201 - 208
226LYSLYSASPASP1BB201 - 208201 - 208
236LYSLYSASPASP1CC201 - 208201 - 208
246LYSLYSASPASP1DD201 - 208201 - 208

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Components

#1: Protein
Deoxynucleoside kinase / / Deoxyribonucleoside kinase / Dm-dNK / Multispecific deoxynucleoside kinase


Mass: 26907.691 Da / Num. of mol.: 4 / Fragment: residues 1-230 / Mutation: N64D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dnk / 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-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.7 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, lithium sulphate, mPEG 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 14, 2003
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→44.72 Å / Num. obs: 65654 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 4.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OE0

1oe0


Resolution: 2.2→44.72 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.141 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.254 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23695 2763 5.1 %RANDOM
Rwork0.21202 ---
obs0.21329 51654 99.94 %-
all-65654 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.736 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20.54 Å2
2---2.4 Å20 Å2
3---2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6576 0 117 194 6887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216848
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9729282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4225786
X-RAY DIFFRACTIONr_chiral_restr0.0810.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025092
X-RAY DIFFRACTIONr_nbd_refined0.2020.22898
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2303
X-RAY DIFFRACTIONr_metal_ion_refined0.1540.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.210
X-RAY DIFFRACTIONr_mcbond_it0.8311.53950
X-RAY DIFFRACTIONr_mcangle_it1.63926424
X-RAY DIFFRACTIONr_scbond_it2.45432898
X-RAY DIFFRACTIONr_scangle_it4.1514.52858
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1561tight positional00.01
2B1561tight positional00.01
3C1561tight positional00.01
4D1561tight positional00.01
1A41medium positional0.790.5
2B41medium positional0.540.5
3C41medium positional0.630.5
4D41medium positional0.660.5
1A1561tight thermal0.130.5
2B1561tight thermal0.130.5
3C1561tight thermal0.140.5
4D1561tight thermal0.140.5
1A41medium thermal0.392
2B41medium thermal0.512
3C41medium thermal0.592
4D41medium thermal0.412
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 207
Rwork0.249 3768

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