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- PDB-6pwz: Crystal structure of human uridine-cytidine kinase 2 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6pwz
TitleCrystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine
ComponentsUridine-cytidine kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / uridine cytidine kinase / nucleotide binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


uridine/cytidine kinase / CTP salvage / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / cellular response to oxygen levels / feeding behavior / response to axon injury / ATP binding ...uridine/cytidine kinase / CTP salvage / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / cellular response to oxygen levels / feeding behavior / response to axon injury / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Uridine kinase-like / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2'-azidocytidine / PHOSPHATE ION / Uridine-cytidine kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCuthbert, B.J. / Goulding, C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1R21MH113062 United States
CitationJournal: To Be Published
Title: Incorporation of novel azido-nucleotides into RNA
Authors: Nainar, S. / Cuthbert, B.J. / Goulding, C.W. / Spitale, R.C.
History
DepositionJul 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Uridine-cytidine kinase 2
B: Uridine-cytidine kinase 2
C: Uridine-cytidine kinase 2
D: Uridine-cytidine kinase 2
E: Uridine-cytidine kinase 2
F: Uridine-cytidine kinase 2
G: Uridine-cytidine kinase 2
H: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,20149
Polymers224,8718
Non-polymers4,33041
Water5,801322
1
A: Uridine-cytidine kinase 2
D: Uridine-cytidine kinase 2
F: Uridine-cytidine kinase 2
G: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,55825
Polymers112,4354
Non-polymers2,12321
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-79 kcal/mol
Surface area37810 Å2
MethodPISA
2
B: Uridine-cytidine kinase 2
C: Uridine-cytidine kinase 2
E: Uridine-cytidine kinase 2
H: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,64324
Polymers112,4354
Non-polymers2,20820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-76 kcal/mol
Surface area37760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.730, 84.740, 153.579
Angle α, β, γ (deg.)90.000, 95.360, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Uridine-cytidine kinase 2 / UCK 2 / Cytidine monophosphokinase 2 / Testis-specific protein TSA903 / Uridine monophosphokinase 2


Mass: 28108.830 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCK2, UMPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZX2, uridine/cytidine kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P6D / 2'-azidocytidine


Mass: 269.237 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C9H13N6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, pH 6.5, 25% pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→83.2 Å / Num. obs: 48286 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 69.63 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.057 / Rrim(I) all: 0.081 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 4783 / CC1/2: 0.619 / Rpim(I) all: 0.432 / Rrim(I) all: 0.611 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6N55

6n55


Resolution: 3→83.2 Å / SU ML: 0.3918 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.985
RfactorNum. reflection% reflection
Rfree0.2539 1119 2.32 %
Rwork0.1973 --
obs0.1986 48261 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 62.58 Å2
Refinement stepCycle: LAST / Resolution: 3→83.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13066 0 277 322 13665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003213536
X-RAY DIFFRACTIONf_angle_d0.699118316
X-RAY DIFFRACTIONf_chiral_restr0.07742156
X-RAY DIFFRACTIONf_plane_restr0.00562334
X-RAY DIFFRACTIONf_dihedral_angle_d5.94138463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.140.32781395873X-RAY DIFFRACTION99.83
3.14-3.30.31971395811X-RAY DIFFRACTION99.82
3.3-3.510.27661390.21145894X-RAY DIFFRACTION99.83
3.51-3.780.23511390.16875829X-RAY DIFFRACTION99.83
3.78-4.160.24191400.17115894X-RAY DIFFRACTION99.9
4.16-4.760.21961380.15815891X-RAY DIFFRACTION99.85
4.76-60.24431410.20725932X-RAY DIFFRACTION99.82
6-83.20.26151446018X-RAY DIFFRACTION99.42

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