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- PDB-6n55: Crystal structure of human uridine-cytidine kinase 2 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6n55
TitleCrystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidouridine
ComponentsUridine-cytidine kinase 2
KeywordsCYTOSOLIC PROTEIN / Uridine-cytidine kinase 2 / UCK2 / Kinase / Complex / Azide
Function / homology
Function and homology information


uridine/cytidine kinase / CTP salvage / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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
PHOSPHATE ION / 2'-azido-2'-deoxyuridine / Uridine-cytidine kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.085 Å
AuthorsCuthbert, B.J. / Nainar, S. / Spitale, R.C. / 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: Nat.Methods / Year: 2020
Title: An optimized chemical-genetic method for cell-specific metabolic labeling of RNA.
Authors: Nainar, S. / Cuthbert, B.J. / Lim, N.M. / England, W.E. / Ke, K. / Sophal, K. / Quechol, R. / Mobley, D.L. / Goulding, C.W. / Spitale, R.C.
History
DepositionNov 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation
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.title / _citation.year
Revision 1.2Feb 19, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 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

Downloads & links

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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)232,21646
Polymers228,1628
Non-polymers4,05438
Water3,315184
1
A: Uridine-cytidine kinase 2
C: Uridine-cytidine kinase 2
F: Uridine-cytidine kinase 2
H: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,92722
Polymers114,0814
Non-polymers1,84618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-74 kcal/mol
Surface area36590 Å2
MethodPISA
2
B: Uridine-cytidine kinase 2
E: Uridine-cytidine kinase 2
G: Uridine-cytidine kinase 2
hetero molecules

D: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,28924
Polymers114,0814
Non-polymers2,20820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area10450 Å2
ΔGint-72 kcal/mol
Surface area36290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.747, 85.764, 153.367
Angle α, β, γ (deg.)90.00, 95.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28520.283 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.: 27 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-UZ0 / 2'-azido-2'-deoxyuridine


Mass: 269.214 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11N5O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50 mM BIS-TRIS pH 6.5, 25 mM ammonium sulfate, 32% pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 198 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 43747 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.986 / Rpim(I) all: 0.055 / Rrim(I) all: 0.105 / Rsym value: 0.089 / Χ2: 1.878 / Net I/σ(I): 22.4
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.85 / Num. unique obs: 2171 / CC1/2: 0.74 / Rpim(I) all: 0.389 / Rrim(I) all: 0.723 / Rsym value: 0.607 / Χ2: 0.724 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UJ2

1uj2


Resolution: 3.085→38.5 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 2211 5.06 %
Rwork0.2111 --
obs0.2136 43704 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.085→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12745 0 259 184 13188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213193
X-RAY DIFFRACTIONf_angle_d0.56417869
X-RAY DIFFRACTIONf_dihedral_angle_d8.0459684
X-RAY DIFFRACTIONf_chiral_restr0.0792125
X-RAY DIFFRACTIONf_plane_restr0.0042270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0851-3.15210.371950.31172008X-RAY DIFFRACTION76
3.1521-3.22540.32051270.27132590X-RAY DIFFRACTION100
3.2254-3.3060.33961510.26512653X-RAY DIFFRACTION100
3.306-3.39540.29121400.242590X-RAY DIFFRACTION100
3.3954-3.49520.31541390.21772616X-RAY DIFFRACTION100
3.4952-3.6080.27551370.21822641X-RAY DIFFRACTION100
3.608-3.73680.29791230.22648X-RAY DIFFRACTION100
3.7368-3.88630.23861260.21082620X-RAY DIFFRACTION100
3.8863-4.0630.2491470.20812624X-RAY DIFFRACTION100
4.063-4.27690.21521260.18542654X-RAY DIFFRACTION100
4.2769-4.54450.23021670.17182598X-RAY DIFFRACTION100
4.5445-4.89480.23361510.17512615X-RAY DIFFRACTION100
4.8948-5.38610.26511450.20812647X-RAY DIFFRACTION100
5.3861-6.16280.2591440.23732651X-RAY DIFFRACTION100
6.1628-7.7540.26641420.2422656X-RAY DIFFRACTION100
7.754-38.50280.24241510.20212682X-RAY DIFFRACTION98

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