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- PDB-2b8t: Crystal structure of Thymidine Kinase from U.urealyticum in compl... -

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Basic information

Entry
Database: PDB / ID: 2b8t
TitleCrystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine
ComponentsThymidine kinase
KeywordsTRANSFERASE / DEOXYRIBONUCLEOSIDE KINASE / ZINC-BINDING DOMAIN / TK1 / UU-TK / THYMIDINE
Function / homology
Function and homology information


thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / zinc ion binding / ATP binding / cytoplasm
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE / Thymidine kinase
Similarity search - Component
Biological speciesUreaplasma parvum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKosinska, U. / Carnrot, C. / Eriksson, S. / Wang, L. / Eklund, H.
CitationJournal: FEBS Lett. / Year: 2005
Title: Structure of the substrate complex of thymidine kinase from Ureaplasma urealyticum and investigations of possible drug targets for the enzyme
Authors: Kosinska, U. / Carnrot, C. / Eriksson, S. / Wang, L. / Eklund, H.
History
DepositionOct 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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_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_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: Thymidine kinase
B: Thymidine kinase
C: Thymidine kinase
D: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,11413
Polymers101,7614
Non-polymers1,3539
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-44 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.158, 115.649, 64.474
Angle α, β, γ (deg.)90.00, 101.02, 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

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYSAA12 - 4912 - 49
21GLYGLYLYSLYSBB12 - 4912 - 49
31GLYGLYLYSLYSCC12 - 4912 - 49
41GLYGLYLYSLYSDD12 - 4912 - 49
52VALVALPHEPHEAA69 - 21369 - 213
62VALVALPHEPHEBB69 - 21369 - 213
72VALVALPHEPHECC69 - 21369 - 213
82VALVALPHEPHEDD69 - 21369 - 213
DetailsThe contents in the asymmetric unit represents the biological assembly i.e. a tetramer.

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Components

#1: Protein
Thymidine kinase /


Mass: 25440.229 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ureaplasma parvum (bacteria) / Gene: tdk / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q9PPP5, thymidine kinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE / Thymidine


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N2O5
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 15% PEG3350, 0.3 M Ammonium formate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2005 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→26.95 Å / Num. all: 54540 / Num. obs: 54484 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym value
2-2.114.30.4241.80.424
2.11-2.244.30.2932.60.293
2.24-2.394.40.213.50.21
2.39-2.584.40.1514.80.151
2.58-2.834.40.1066.70.106
2.83-3.164.40.0768.70.076
3.16-3.655.30.0728.30.072
3.65-4.4780.0628.90.062
4.47-6.328.10.06290.062
6.32-26.927.80.0925.80.092

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Phasing

Phasing MRRfactor: 0.383 / Cor.coef. Fo:Fc: 0.616
Highest resolutionLowest resolution
Rotation3 Å26.92 Å
Translation3 Å26.92 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
ProDCdata collection
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XMR

1xmr
PDB Unreleased entry


Resolution: 2→26.95 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.921 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2769 5.1 %RANDOM
Rwork0.19535 ---
obs0.19741 51687 98.96 %-
all-54456 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.885 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.16 Å2
2--1.83 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2→26.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6380 0 80 230 6690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226600
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.041.9628913
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1785791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99124.286315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.424151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4631534
X-RAY DIFFRACTIONr_chiral_restr0.0720.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024978
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.22793
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24575
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2368
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3671.54120
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.63126434
X-RAY DIFFRACTIONr_scbond_it0.91232832
X-RAY DIFFRACTIONr_scangle_it1.3954.52479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A732medium positional0.190.5
2B732medium positional0.190.5
3C732medium positional0.180.5
4D732medium positional0.250.5
1A736loose positional0.565
2B736loose positional0.635
3C736loose positional0.595
4D736loose positional0.655
1A732medium thermal0.412
2B732medium thermal0.432
3C732medium thermal0.332
4D732medium thermal0.382
1A736loose thermal0.9510
2B736loose thermal0.8610
3C736loose thermal0.9310
4D736loose thermal0.9410
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 194 -
Rwork0.257 3373 -
obs--98.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2816-0.4011-0.32421.8658-0.34211.23890.071-0.0321-0.3674-0.0245-0.00150.1640.1376-0.1932-0.0695-0.15970.0032-0.025-0.11350.0272-0.083-6.3557-8.633927.1632
22.2095-2.3286-2.58932.4853.300613.59320.0378-0.4610.13180.21980.0921-0.4011-0.34530.0445-0.1298-0.1307-0.1137-0.02650.12180.01640.0147-19.63950.946635.7198
34.87950.5102-1.58751.8074-2.10665.40310.0801-0.62340.76950.15910.02110.0896-0.5242-0.134-0.1012-0.03370.05550.0244-0.0551-0.0998-0.0381-3.37312.863239.181
416.24048.3733.596732.6134-4.37157.8055-0.1286-1.73341.5273-0.3242-0.44970.1948-0.9721-0.26160.57840.08640.00460.05250.1906-0.24520.017515.797611.287951.7534
52.04490.2352-0.24022.09420.76422.00150.13370.35880.6218-0.19120.0870.035-0.5829-0.1463-0.22070.05480.06510.0288-0.03880.08640.01092.202813.86757.0462
63.9982-0.2112-1.58942.6591-2.04398.0392-0.00220.7963-0.5102-0.3634-0.05190.20590.4689-0.53020.0541-0.0068-0.0108-0.04170.1093-0.0943-0.11810.5399-7.8824-4.6565
77.81943.3822-2.091710.6337-3.14564.21250.37421.3108-0.9911-1.2337-0.4760.32151.3933-0.10890.10170.41030.1277-0.10750.2058-0.20380.047421.6491-15.1081-9.0856
81.86310.048-0.15151.39040.10021.66260.0825-0.36530.06750.1548-0.0549-0.012-0.1370.1512-0.0276-0.16010.008-0.0047-0.0650.0195-0.166619.40830.840336.9784
94.24231.2949-2.9420.47120.105715.3041-0.0642-0.7408-0.7673-0.00560.29590.03960.86970.4192-0.2317-0.15040.0389-0.06180.14940.0911-0.058932.2416-7.256332.6239
103.1777-0.3206-0.13482.5028-1.02776.79470.07-0.2657-0.77040.0937-0.0351-0.06180.59710.1577-0.0349-0.07330.0392-0.0118-0.18080.10930.073514.4316-23.125832.8321
119.34874.64673.430118.581411.795421.36960.1348-0.5004-1.42120.0551-0.15550.08131.2799-0.13580.02080.0201-0.0117-0.0111-0.14810.17810.4198-7.9404-25.904733.8669
122.1018-0.29580.09131.42490.09023.5610.04390.2412-0.1432-0.2591-0.0533-0.10220.13350.21650.0093-0.11960.04820.0061-0.08750.0014-0.161323.6624-5.96016.9238
130.64520.30520.8219.035912.154316.61420.29280.31520.0344-0.86470.2132-0.4597-0.88471.0784-0.506-0.11310.03910.05520.0280.0358-0.051235.7111-4.604415.7533
144.4836-0.1613-1.08024.9133-0.65799.9747-0.01710.28710.7824-0.282-0.0772-0.737-0.88461.05540.09430.0999-0.12710.0289-0.02730.09060.133628.023518.055611.2159
156.89416.61573.81086.34853.65692.10650.60260.81881.8930.5778-0.7694-0.6744-0.2806-0.78570.16680.48170.1050.13320.04060.27280.701910.083929.92671.6253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 4912 - 49
2X-RAY DIFFRACTION1AA69 - 15069 - 150
3X-RAY DIFFRACTION2AA50 - 6850 - 68
4X-RAY DIFFRACTION3AA151 - 202151 - 202
5X-RAY DIFFRACTION4AA203 - 213203 - 213
6X-RAY DIFFRACTION5BB12 - 5012 - 50
7X-RAY DIFFRACTION5BB69 - 15069 - 150
8X-RAY DIFFRACTION6BB151 - 202151 - 202
9X-RAY DIFFRACTION7BB203 - 213203 - 213
10X-RAY DIFFRACTION8CC12 - 4912 - 49
11X-RAY DIFFRACTION8CC69 - 15069 - 150
12X-RAY DIFFRACTION9CC50 - 5150 - 51
13X-RAY DIFFRACTION9CC60 - 6860 - 68
14X-RAY DIFFRACTION10CC151 - 202151 - 202
15X-RAY DIFFRACTION11CC203 - 213203 - 213
16X-RAY DIFFRACTION12DD12 - 4912 - 49
17X-RAY DIFFRACTION12DD69 - 15069 - 150
18X-RAY DIFFRACTION13DD54 - 6654 - 66
19X-RAY DIFFRACTION14DD151 - 201151 - 201
20X-RAY DIFFRACTION15DD203 - 213203 - 213

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