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- PDB-5x8j: K16M mutant of thermus thermophilus HB8 thymidylate kinase -

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Basic information

Entry
Database: PDB / ID: 5x8j
TitleK16M mutant of thermus thermophilus HB8 thymidylate kinase
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Nucleotide monophosphate kinase
Function / homology
Function and homology information


dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / ATP binding / cytosol
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
FORMIC ACID / Thymidylate kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 3, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,1615
Polymers44,0232
Non-polymers1383
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-18 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.643, 47.180, 152.108
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: 22011.559 Da / Num. of mol.: 2 / Mutation: K16M
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 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHX3, dTMP kinase
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.9 Å3/Da / Density % sol: 35.29 %
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 RUH3R / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.8→47.18 Å / Num. obs: 30458 / % possible obs: 94.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.08 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.84 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X7J

5x7j


Resolution: 1.8→47.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.819 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23016 1476 4.9 %RANDOM
Rwork0.18354 ---
obs0.18578 28903 94.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.916 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å2-0 Å2
2---0.24 Å20 Å2
3---0.76 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 0 9 221 3077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192942
X-RAY DIFFRACTIONr_bond_other_d0.0020.022930
X-RAY DIFFRACTIONr_angle_refined_deg1.8272.0173984
X-RAY DIFFRACTIONr_angle_other_deg1.01936726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5125373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.16721.04125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70915493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6811542
X-RAY DIFFRACTIONr_chiral_restr0.1010.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02639
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_it0.8151.1011477
X-RAY DIFFRACTIONr_mcbond_other0.8161.1021478
X-RAY DIFFRACTIONr_mcangle_it1.4271.6391840
X-RAY DIFFRACTIONr_mcangle_other1.4271.6411841
X-RAY DIFFRACTIONr_scbond_it0.8971.2161465
X-RAY DIFFRACTIONr_scbond_other0.8731.211460
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4681.7772141
X-RAY DIFFRACTIONr_long_range_B_refined3.9413.5883242
X-RAY DIFFRACTIONr_long_range_B_other3.87413.3163199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 74 -
Rwork0.238 1391 -
obs--62.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.01570.39660.19680.68580.46440.32380.01820.0752-0.03810.002-0.03240.025-0.0129-0.02030.01420.0799-0.00540.01090.0594-0.02580.01289.67750.98811.316
20.25650.2823-0.05750.5070.23430.5053-0.00110.02160.0059-0.00130.02810.0086-0.05580.0351-0.0270.1036-0.00720.01680.0401-0.01050.020729.20577.12326.889
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 198
2X-RAY DIFFRACTION2B2 - 197

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