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- PDB-5fuy: catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP -

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Basic information

Entry
Database: PDB / ID: 5fuy
Titlecatalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP
ComponentsTHYMDINE KINASE
KeywordsTRANSFERASE / THYMIDINE KINASE / T.BRUCEI / TBTK / TKII / DTMP
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 / Chem-QBT / thymidine kinase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.mon_nstd_flag / _database_2.pdbx_DOI ..._chem_comp.mon_nstd_flag / _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 1.3Nov 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
C: THYMDINE KINASE
D: THYMDINE KINASE
E: THYMDINE KINASE
F: THYMDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,35424
Polymers123,4476
Non-polymers2,90818
Water73941
1
A: THYMDINE KINASE
B: THYMDINE KINASE
C: THYMDINE KINASE
D: THYMDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,23616
Polymers82,2984
Non-polymers1,93812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-78.6 kcal/mol
Surface area24790 Å2
MethodPISA
2
E: THYMDINE KINASE
F: THYMDINE KINASE
hetero molecules

E: THYMDINE KINASE
F: THYMDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,23616
Polymers82,2984
Non-polymers1,93812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11260 Å2
ΔGint-71.7 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.614, 96.999, 304.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
THYMDINE KINASE


Mass: 20574.455 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, RESIDUES 204-383 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Strain: LISTER427 / Plasmid: 11347 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Variant (production host): SF9 / References: UniProt: Q38CF2, thymidine kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-QBT / [(2R,3S,5R)-3-HYDROXY-5-[(5S)-5-METHYL-2,4-DIOXO-1,3-DIAZINAN-1-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE


Type: DNA linking / Mass: 324.224 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N2O8P
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7
Details: 0.15 M DL-MALIC ACID PH 7.0, 20% (W/V) PEG 3350, 1 MM TMP, 1 MM APPNHP, 3 MM MGCL2, PLUS SEEDING

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→65.02 Å / Num. obs: 31168 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7

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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 5FUV

5fuv


Resolution: 2.8→152.22 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.383 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24344 1570 5.1 %RANDOM
Rwork0.20847 ---
obs0.21019 29477 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.494 Å2
Baniso -1Baniso -2Baniso -3
1-7.04 Å20 Å20 Å2
2---4.64 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→152.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7404 0 162 41 7607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197701
X-RAY DIFFRACTIONr_bond_other_d0.010.027043
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.97210437
X-RAY DIFFRACTIONr_angle_other_deg1.6043.00316069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6295976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.50322.949312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.006151201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.221558
X-RAY DIFFRACTIONr_chiral_restr0.0750.21199
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028642
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021740
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_it5.1136.6773940
X-RAY DIFFRACTIONr_mcbond_other5.1136.6763939
X-RAY DIFFRACTIONr_mcangle_it7.7310.0054904
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4977.0033761
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 135 -
Rwork0.349 2191 -
obs--98.35 %

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