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- PDB-5x8d: D90L mutant of thermus thermophilus HB8 thymidylate kinase -

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Basic information

Entry
Database: PDB / ID: 5x8d
TitleD90L mutant of thermus thermophilus HB8 thymidylate kinase
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Nucleotide monophosphate 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
DI(HYDROXYETHYL)ETHER / Thymidylate kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsChaudhary, S.K. / Jeyakanthan, J. / Sekar, K.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structural and functional roles of dynamically correlated residues in thymidylate kinase.
Authors: Chaudhary, S.K. / Jeyakanthan, J. / Sekar, K.
History
DepositionMar 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
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.year
Revision 1.2Nov 21, 2018Group: 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,4319
Polymers44,0152
Non-polymers4167
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-37 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.800, 47.320, 153.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thymidylate kinase / / dTMP kinase


Mass: 22007.613 Da / Num. of mol.: 2 / Mutation: D90L
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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHX3, dTMP kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.1 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.2M MgCl2.6H2O, 0.1 M Tris hydrochloride, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.26→76.64 Å / Num. obs: 15291 / % possible obs: 91.9 % / Redundancy: 7.9 % / Net I/σ(I): 9.3
Reflection shellResolution: 2.26→2.33 Å

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X7J

5x7j


Resolution: 2.26→76.64 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.543 / ESU R Free: 0.281
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 721 4.7 %RANDOM
Rwork0.2181 ---
obs0.2203 15242 91.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.42 Å2 / Biso mean: 21.8676 Å2 / Biso min: 6.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å2-0 Å2
2---0.3 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.26→76.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 0 25 82 2951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192931
X-RAY DIFFRACTIONr_bond_other_d00.022931
X-RAY DIFFRACTIONr_angle_refined_deg1.2922.0223961
X-RAY DIFFRACTIONr_angle_other_deg3.61636731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2865367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87421.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1515487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5621540
X-RAY DIFFRACTIONr_chiral_restr0.0640.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213200
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02622
X-RAY DIFFRACTIONr_mcbond_it0.9132.1431474
X-RAY DIFFRACTIONr_mcbond_other0.9122.1431474
X-RAY DIFFRACTIONr_mcangle_it1.6783.2011836
LS refinement shellResolution: 2.259→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 55 -
Rwork0.349 961 -
all-1016 -
obs--84.6 %

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