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- PDB-5x7j: Crystal structure of thymidylate kinase from thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 5x7j
TitleCrystal structure of thymidylate kinase 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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsChaudhary, S.K. / Jeyakanthan, J. / Sekar, K.
CitationJournal: Int. J. Biol. Macromol. / Year: 2019
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 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)45,02326
Polymers44,0192
Non-polymers1,00424
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-239 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.470, 80.210, 122.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 (strain HB8 / ATCC 27634 / DSM 579) (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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.3 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 0.2M CaCl2.2H2O, 20% w/v, PEG 3350

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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 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.83→40.88 Å / Num. obs: 34412 / % possible obs: 96.8 % / Redundancy: 8.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.8
Reflection shellResolution: 1.83→1.87 Å / Num. unique obs: 1060 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBR

2pbr


Resolution: 1.84→40.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.865 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21996 1667 4.9 %RANDOM
Rwork0.17614 ---
obs0.17831 32679 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.198 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.45 Å2-0 Å2
3----0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.84→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 36 189 3200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193046
X-RAY DIFFRACTIONr_bond_other_d0.0020.023055
X-RAY DIFFRACTIONr_angle_refined_deg1.882.0184113
X-RAY DIFFRACTIONr_angle_other_deg1.06636999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8955380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.62720.551127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87815508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2621547
X-RAY DIFFRACTIONr_chiral_restr0.1170.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213328
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02661
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_it1.9211.8991530
X-RAY DIFFRACTIONr_mcbond_other1.9171.8991530
X-RAY DIFFRACTIONr_mcangle_it2.8612.8231905
X-RAY DIFFRACTIONr_mcangle_other2.8622.8241906
X-RAY DIFFRACTIONr_scbond_it2.6532.2391516
X-RAY DIFFRACTIONr_scbond_other2.6452.2391516
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0853.2362209
X-RAY DIFFRACTIONr_long_range_B_refined6.31423.3463334
X-RAY DIFFRACTIONr_long_range_B_other6.02523.2193308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.842→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 119 -
Rwork0.407 2211 -
obs--91.66 %

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