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- PDB-5uiv: Structure of Thymidylate Kinase from Candida albicans Reveals Ori... -

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Basic information

Entry
Database: PDB / ID: 5uiv
TitleStructure of Thymidylate Kinase from Candida albicans Reveals Origin of Broad Substrate Specificity and a Novel Structural Element.
ComponentsBifunctional thymidylate/uridylate kinase
KeywordsTRANSFERASE / Thymidylate kinase / Candida albicans
Function / homology
Function and homology information


UMP/dUMP kinase activity / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 / dTMP kinase
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSinha, K. / Rule, G.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Mellon College of Science (Carnegie Mellon University) United States
CitationJournal: Biochemistry / Year: 2017
Title: The Structure of Thymidylate Kinase from Candida albicans Reveals a Unique Structural Element.
Authors: Sinha, K. / Rule, G.S.
History
DepositionJan 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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: Bifunctional thymidylate/uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6885
Polymers25,8901
Non-polymers7984
Water1,38777
1
A: Bifunctional thymidylate/uridylate kinase
hetero molecules

A: Bifunctional thymidylate/uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,37710
Polymers51,7812
Non-polymers1,5968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5250 Å2
ΔGint-73 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.965, 69.965, 116.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Bifunctional thymidylate/uridylate kinase


Mass: 25890.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: CAALFM_C111790WA / Production host: Escherichia coli (E. coli) / References: UniProt: Q59TV7
#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, 1.1 N Sodium Citrate, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.45→60.59 Å / Num. obs: 11717 / % possible obs: 92.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 1.89
Reflection shellResolution: 2.45→2.55 Å / Rmerge(I) obs: 0.278

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLM7.2.0data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tmk

3tmk


Resolution: 2.45→60.59 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.425 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21805 606 5.2 %RANDOM
Rwork0.16788 ---
obs0.17049 11056 92.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.429 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.45→60.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 50 77 1944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021906
X-RAY DIFFRACTIONr_bond_other_d0.0020.021823
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9992591
X-RAY DIFFRACTIONr_angle_other_deg1.03934210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.32125.7389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07515351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.711158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022115
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02422
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_it2.8613.47904
X-RAY DIFFRACTIONr_mcbond_other2.8583.469903
X-RAY DIFFRACTIONr_mcangle_it4.3495.2011129
X-RAY DIFFRACTIONr_mcangle_other4.3485.2021130
X-RAY DIFFRACTIONr_scbond_it3.5643.7581002
X-RAY DIFFRACTIONr_scbond_other3.5623.7581003
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5575.4921462
X-RAY DIFFRACTIONr_long_range_B_refined7.22127.0742167
X-RAY DIFFRACTIONr_long_range_B_other7.19627.0422148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.447→2.511 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 35 -
Rwork0.244 480 -
obs--54.9 %

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