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- PDB-5fuv: catalytic domain of Thymidine kinase from Trypanosoma brucei with dThd -

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Basic information

Entry
Database: PDB / ID: 5fuv
Titlecatalytic domain of Thymidine kinase from Trypanosoma brucei with dThd
ComponentsTHYMDINE KINASE
KeywordsTRANSFERASE / THYMIDINE KINASE / T.BRUCEI / TBTK / TKII / DTHD
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide salvage / thymidine metabolic process / thymidine kinase / thymidine kinase activity / pyrimidine nucleotide metabolic process / nucleobase-containing small molecule interconversion / DNA biosynthetic process / mitochondrion / ATP binding / metal ion binding ...pyrimidine deoxyribonucleotide salvage / thymidine metabolic process / thymidine kinase / thymidine kinase activity / pyrimidine nucleotide metabolic process / nucleobase-containing small molecule interconversion / DNA biosynthetic process / mitochondrion / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich ...Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / THYMIDINE / thymidine kinase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTimm, J. / Valente, M. / Castillo-Acosta, V. / Balzarini, T. / Nettleship, J.E. / Rada, H. / Wilson, K.S. / Gonzalez-Pacanowska, D.
CitationJournal: Mol.Microbiol. / Year: 2016
Title: Cell Cycle Regulation and Novel Structural Features of Thymidine Kinase, an Essential Enzyme in Trypanosoma Brucei.
Authors: Valente, M. / Timm, J. / Castillo-Acosta, V.M. / Ruiz-Perez, L.M. / Balzarini, T. / Nettleship, J.E. / Bird, L.E. / Rada, H. / Wilson, K.S. / Gonzalez-Pacanowska, D.
History
DepositionJan 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _atom_site.occupancy / _chem_comp.type ..._atom_site.occupancy / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMDINE KINASE
B: THYMDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,99310
Polymers41,0072
Non-polymers9878
Water1,54986
1
A: THYMDINE KINASE
B: THYMDINE KINASE
hetero molecules

A: THYMDINE KINASE
B: THYMDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,98720
Polymers82,0144
Non-polymers1,97316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area11930 Å2
ΔGint-6.4 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.680, 114.680, 105.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-1387-

PO4

21A-1387-

PO4

31A-2011-

HOH

41B-2009-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein THYMDINE KINASE


Mass: 20503.375 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 204-383 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Variant: LISTER427 / Plasmid: 11347 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q38CF2, thymidine kinase

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Non-polymers , 5 types, 94 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.77 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M HEPES PH 7.0, 0.8 M SUCCINIC ACID 1 MM TMP, 1 MM APPNHP, 3 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→44.25 Å / Num. obs: 31864 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W4R

1w4r


Resolution: 2.3→114.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.613 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20745 1708 5.4 %RANDOM
Rwork0.17869 ---
obs0.18016 30146 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.235 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2---0.77 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→114.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 59 86 2733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192692
X-RAY DIFFRACTIONr_bond_other_d0.0090.022519
X-RAY DIFFRACTIONr_angle_refined_deg2.2171.973626
X-RAY DIFFRACTIONr_angle_other_deg1.5733.0035764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23622.931116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08815451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6951523
X-RAY DIFFRACTIONr_chiral_restr0.1230.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022994
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02613
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9855.6891344
X-RAY DIFFRACTIONr_mcbond_other5.9795.6851343
X-RAY DIFFRACTIONr_mcangle_it8.0328.5021673
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.7356.1961348
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 107 -
Rwork0.269 2216 -
obs--99.7 %

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