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- PDB-5xb3: ADP-dTMP bound Crystal structure of thymidylate kinase (aq_969) f... -

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Basic information

Entry
Database: PDB / ID: 5xb3
TitleADP-dTMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Kinase / Complex / Nucleotide Binding
Function / homology
Function and homology information


dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding / cytosol / cytoplasm
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
ADENOSINE-5'-DIPHOSPHATE / THYMIDINE-5'-PHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBiswas, A. / Jeyakanthan, J. / Sekar, K.
CitationJournal: FEBS J. / Year: 2017
Title: Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate
Authors: Biswas, A. / Shukla, A. / Chaudhary, S.K. / Santhosh, R. / Jeyakanthan, J. / Sekar, K.
History
DepositionMar 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,3056
Polymers44,8062
Non-polymers1,4994
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-36 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.540, 52.980, 53.780
Angle α, β, γ (deg.)90.97, 90.69, 109.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thymidylate kinase / dTMP kinase


Mass: 22402.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: tmk, aq_969 / Production host: Escherichia coli (E. coli) / References: UniProt: O67099, dTMP kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7
Details: 0.2M Ammonium citrate tribasic, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.77→53.76 Å / Num. obs: 39574 / % possible obs: 92 % / Redundancy: 5 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.4
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.604 / Num. unique obs: 5334 / CC1/2: 0.816 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBR

2pbr


Resolution: 1.77→53.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.656 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21263 1844 4.7 %RANDOM
Rwork0.16252 ---
obs0.16485 37728 91.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.547 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0.25 Å21.13 Å2
2--0.41 Å21.59 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.77→53.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 96 283 3459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193279
X-RAY DIFFRACTIONr_bond_other_d0.0020.023242
X-RAY DIFFRACTIONr_angle_refined_deg2.0822.0414432
X-RAY DIFFRACTIONr_angle_other_deg1.07237498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84124.861144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31915644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9351521
X-RAY DIFFRACTIONr_chiral_restr0.1210.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02668
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_it1.7491.8551564
X-RAY DIFFRACTIONr_mcbond_other1.741.8531563
X-RAY DIFFRACTIONr_mcangle_it2.4232.7711956
X-RAY DIFFRACTIONr_mcangle_other2.4232.7731957
X-RAY DIFFRACTIONr_scbond_it2.8422.1471715
X-RAY DIFFRACTIONr_scbond_other2.8262.1451711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2423.092462
X-RAY DIFFRACTIONr_long_range_B_refined5.09222.3383792
X-RAY DIFFRACTIONr_long_range_B_other5.02622.0093725
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.771→1.817 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 121 -
Rwork0.259 2384 -
obs--79.02 %

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