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- PDB-2qqe: Thymidine Kinase from Thermotoga Maritima in complex with Thymidine -

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Basic information

Entry
Database: PDB / ID: 2qqe
TitleThymidine Kinase from Thermotoga Maritima in complex with Thymidine
ComponentsThymidine kinase
KeywordsTRANSFERASE / TmTK in complex with thymidine / Close conformation / ATP-binding / Cytoplasm / DNA synthesis / Kinase / Nucleotide-binding
Function / homology
Function and homology information


thymidine metabolic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / zinc ion binding / ATP binding / identical protein 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 / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSegura-Pena, D. / Lichter, J. / Trani, M. / Konrad, M. / Lavie, A. / Lutz, S.
CitationJournal: Structure / Year: 2007
Title: Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes.
Authors: Segura-Pena, D. / Lichter, J. / Trani, M. / Konrad, M. / Lavie, A. / Lutz, S.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9856
Polymers41,3702
Non-polymers6154
Water88349
1
A: Thymidine kinase
B: Thymidine kinase
hetero molecules

A: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,97012
Polymers82,7404
Non-polymers1,2318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area8400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.590, 52.820, 59.310
Angle α, β, γ (deg.)90.00, 107.90, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSAA2 - 402 - 40
21SERSERLYSLYSBB2 - 402 - 40
32VALVALALAALAAA58 - 15558 - 155
42VALVALALAALABB58 - 15558 - 155
53ILEILELYSLYSAA161 - 181161 - 181
63ILEILELYSLYSBB161 - 181161 - 181
DetailsThe tetrameric biological assembly is generated from the dimer in the assimetric unit by the operation (-x, y, -z)

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Components

#1: Protein Thymidine kinase /


Mass: 20684.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tdk / Plasmid: pET14B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9WYN2, thymidine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 60-65% MPD + 0.1 M Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2006 / Details: mirrors
RadiationMonochromator: monocromator SI (111) sagittal focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→12 Å / Num. all: 24026 / Num. obs: 23671 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 31.7 Å2 / Rsym value: 0.0762 / Net I/σ(I): 13
Reflection shellResolution: 1.9→2.07 Å / Redundancy: 3.5 % / Num. unique all: 3667 / Rsym value: 0.334 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→12 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / SU B: 4.838 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28571 2528 10.1 %RANDOM
Rwork0.23556 ---
obs0.24076 22601 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.48 Å2
2---0.7 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 36 49 2589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222578
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9973472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96624.257101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37915473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.71512
X-RAY DIFFRACTIONr_chiral_restr0.1080.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021848
X-RAY DIFFRACTIONr_nbd_refined0.2150.21171
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3520.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.28
X-RAY DIFFRACTIONr_mcbond_it0.9491.51629
X-RAY DIFFRACTIONr_mcangle_it1.57922561
X-RAY DIFFRACTIONr_scbond_it2.5731061
X-RAY DIFFRACTIONr_scangle_it3.9194.5911
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1216 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.320.5
medium thermal0.82
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 156 -
Rwork0.289 1665 -
obs--98.27 %

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