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- PDB-5fuw: catalytic domain of Thymidine kinase from Trypanosoma brucei with... -

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Basic information

Entry
Database: PDB / ID: 5fuw
Titlecatalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP or dThd
ComponentsTHYMDINE KINASE
KeywordsTRANSFERASE / THYMIDINE KINASE / T.BRUCEI / TBTK / TKII / DTHD / 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 / nucleus ...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 / nucleus / metal ion binding / 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 / thymidine kinase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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_ncs_dom_lim / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _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_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: THYMDINE KINASE
B: THYMDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9899
Polymers41,0072
Non-polymers9827
Water2,648147
1
A: THYMDINE KINASE
B: THYMDINE KINASE
hetero molecules

A: THYMDINE KINASE
B: THYMDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,97818
Polymers82,0144
Non-polymers1,96414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area10290 Å2
ΔGint-63.9 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.999, 114.999, 104.770
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-2016-

HOH

21B-2013-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 204 - 383 / Label seq-ID: 2 - 181

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 / 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, 154 molecules

#2: 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.: 1 / Source method: obtained synthetically / Formula: C10H17N2O8P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.77 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: I02 / Wavelength: 0.9795
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→64.24 Å / Num. obs: 36299 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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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: 2.2→115 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.16 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20126 1757 4.8 %RANDOM
Rwork0.18532 ---
obs0.1861 34470 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.707 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2---1.23 Å20 Å2
3---2.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 0 55 147 2779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192692
X-RAY DIFFRACTIONr_bond_other_d0.0090.022512
X-RAY DIFFRACTIONr_angle_refined_deg2.161.973635
X-RAY DIFFRACTIONr_angle_other_deg1.6363.0035748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6755333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00522.735117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57215454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1051524
X-RAY DIFFRACTIONr_chiral_restr0.1250.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022994
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02620
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_it5.715.3541338
X-RAY DIFFRACTIONr_mcbond_other5.7065.3511337
X-RAY DIFFRACTIONr_mcangle_it7.8177.9931666
X-RAY DIFFRACTIONr_mcangle_other7.8157.9971667
X-RAY DIFFRACTIONr_scbond_it7.5745.9051354
X-RAY DIFFRACTIONr_scbond_other7.4095.8911338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.4638.6351945
X-RAY DIFFRACTIONr_long_range_B_refined12.47251.44511349
X-RAY DIFFRACTIONr_long_range_B_other12.47251.44511350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18368 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 151 -
Rwork0.295 2498 -
obs--99.77 %

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