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- PDB-5zax: Crystal structure of thymidylate kinase in complex with ADP, TDP ... -

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Basic information

Entry
Database: PDB / ID: 5zax
TitleCrystal structure of thymidylate kinase in complex with ADP, TDP and TMP from thermus thermophilus HB8
ComponentsThymidylate kinase
KeywordsTRANSFERASE / NMP kinase
Function / homology
Function and homology information


dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / THYMIDINE-5'-PHOSPHATE / THYMIDINE-5'-DIPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsChaudhary, S.K. / Jeyakanthan, J. / Sekar, K.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Insights into product release dynamics through structural analyses of thymidylate kinase.
Authors: Chaudhary, S.K. / Iyyappan, Y. / Elayappan, M. / Jeyakanthan, J. / Sekar, K.
History
DepositionFeb 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate kinase
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,50717
Polymers44,0192
Non-polymers1,48815
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-137 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.408, 47.658, 152.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thymidylate kinase / / dTMP kinase


Mass: 22009.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: tmk, TTHA1607
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5SHX3, dTMP kinase

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Non-polymers , 6 types, 73 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#6: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.2M MgCl2.6H2O, 0.1M Tris hydrochloride, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.36→18.54 Å / Num. obs: 14849 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.135 / Net I/σ(I): 10.5
Reflection shellResolution: 2.36→2.46 Å / Rmerge(I) obs: 0.453 / CC1/2: 0.847

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X7J

5x7j


Resolution: 2.36→18.54 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.809 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.787 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3239 688 4.7 %RANDOM
Rwork0.2451 ---
obs0.2488 13923 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.58 Å2 / Biso mean: 19.868 Å2 / Biso min: 4.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å2-0 Å2
2---0.86 Å20 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 2.36→18.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 85 58 3050
Biso mean--26.98 15.43 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193042
X-RAY DIFFRACTIONr_bond_other_d00.022979
X-RAY DIFFRACTIONr_angle_refined_deg1.3492.0464137
X-RAY DIFFRACTIONr_angle_other_deg3.60436843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.185373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16321.36125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60815492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5721539
X-RAY DIFFRACTIONr_chiral_restr0.0630.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213301
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02641
X-RAY DIFFRACTIONr_mcbond_it0.7911.9651501
X-RAY DIFFRACTIONr_mcbond_other0.7891.9651501
X-RAY DIFFRACTIONr_mcangle_it1.4392.9311869
LS refinement shellResolution: 2.36→2.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 61 -
Rwork0.37 943 -
all-1004 -
obs--95.71 %

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