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- PDB-2qq0: Thymidine Kinase from Thermotoga Maritima in complex with thymidi... -

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Basic information

Entry
Database: PDB / ID: 2qq0
TitleThymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp
ComponentsThymidine kinase
KeywordsTRANSFERASE / Thymidine Kinase / TmTK / AppNHp / open-conformation / ATP-binding / Cytoplasm / DNA synthesis / Nucleotide-binding
Function / homology
Function and homology information


thymidine metabolic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / 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 / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / THYMIDINE / THYMIDINE-5'-PHOSPHATE / Thymidine kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 25, 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 / Derived calculations
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_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)43,04710
Polymers41,3702
Non-polymers1,6778
Water6,900383
1
A: Thymidine kinase
B: Thymidine kinase
hetero molecules

A: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,09420
Polymers82,7404
Non-polymers3,35516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.160, 59.310, 61.300
Angle α, β, γ (deg.)90.00, 103.02, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe tetrameric biological assembly is generated from the dimer in the assimetric unit by the operation (-x, y, -z)

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 7 types, 391 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2005 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→28 Å / Num. all: 57288 / Num. obs: 54800 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.065 / Net I/σ(I): 13
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.45 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 8115 / Rsym value: 0.32 / % possible all: 88.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.397 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21665 5515 10.1 %RANDOM
Rwork0.17085 ---
obs0.17547 49113 95.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.028 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20.11 Å2
2--0.79 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 100 383 3142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222801
X-RAY DIFFRACTIONr_angle_refined_deg1.6862.0233787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4915333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03824.643112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48415510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9981512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021986
X-RAY DIFFRACTIONr_nbd_refined0.1990.21476
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2384
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.231
X-RAY DIFFRACTIONr_mcbond_it1.0961.51712
X-RAY DIFFRACTIONr_mcangle_it1.7922709
X-RAY DIFFRACTIONr_scbond_it2.89731219
X-RAY DIFFRACTIONr_scangle_it4.6084.51078
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 354 -
Rwork0.24 3045 -
obs--81.71 %

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