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- PDB-3asy: ligand-free structure of uridine kinase from thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 3asy
Titleligand-free structure of uridine kinase from thermus thermophilus HB8
ComponentsUridine kinase
KeywordsTRANSFERASE / cytidine phosphorylation
Function / homology
Function and homology information


uridine/cytidine kinase / CTP salvage / uridine kinase activity / cytidine kinase activity / UMP salvage / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Uridine kinase / Uridine kinase-like / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTomoike, F. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
CitationJournal: Biochemistry / Year: 2011
Title: A Single Amino Acid Limits the Substrate Specificity of Thermus thermophilus Uridine-Cytidine Kinase to Cytidine
Authors: Tomoike, F. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionDec 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine kinase
B: Uridine kinase


Theoretical massNumber of molelcules
Total (without water)47,4192
Polymers47,4192
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-8 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.364, 70.364, 179.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Uridine kinase / / Cytidine monophosphokinase / Uridine monophosphokinase


Mass: 23709.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: udk, TTHA0578 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKR5, uridine/cytidine kinase
#2: 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 40% (v/v) isopropanol, 15%(w/v) PEG 8000, 0.1M imidazole, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2008
RadiationMonochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 18465 / Num. obs: 18465 / Observed criterion σ(F): 0
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 6.4

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: uridine cytidine kinase2 from Homo sapiens

Resolution: 2.4→37.8 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2995 1715 9.3 %random
Rwork0.233 15903 --
all-18465 --
obs-18465 --
Solvent computationBsol: 27.6311 Å2
Displacement parametersBiso mean: 47.0139 Å2
Baniso -1Baniso -2Baniso -3
1--4.483 Å20 Å20 Å2
2---4.483 Å20 Å2
3---8.966 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3186 0 0 82 3268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it5.721.5
X-RAY DIFFRACTIONc_scbond_it8.4522
X-RAY DIFFRACTIONc_mcangle_it7.3962
X-RAY DIFFRACTIONc_scangle_it10.562.4
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2water.param

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