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- PDB-6n54: Crystal structure of human uridine-cytidine kinase 2 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6n54
TitleCrystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine monophosphate
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 / ribosylnicotinamide kinase activity / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / phosphorylation / ATP binding / identical protein binding ...uridine/cytidine kinase / CTP salvage / ribosylnicotinamide kinase activity / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / phosphorylation / ATP binding / identical protein binding / cytoplasm / cytosol
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
Chem-KEA / PHOSPHATE ION / Uridine-cytidine kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.424 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,62015
Polymers57,0412
Non-polymers1,58013
Water2,612145
1
A: Uridine-cytidine kinase 2
B: Uridine-cytidine kinase 2
hetero molecules

A: Uridine-cytidine kinase 2
B: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,24030
Polymers114,0814
Non-polymers3,15926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10600 Å2
ΔGint-102 kcal/mol
Surface area36310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.329, 141.263, 247.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

21A-460-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
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

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Non-polymers , 5 types, 158 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-KEA / 2'-azido-2'-deoxycytidine 5'-(dihydrogen phosphate) / 2'-azidocytidine monophosphate


Mass: 348.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N6O7P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.47 Å3/Da / Density % sol: 64.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Na/K phosphate, 20% PEG 3350

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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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 29839 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.999 / Rpim(I) all: 0.04 / Rrim(I) all: 0.105 / Rsym value: 0.097 / Χ2: 1.764 / Net I/σ(I): 31.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.66 / Num. unique obs: 1456 / CC1/2: 0.724 / Rpim(I) all: 0.437 / Χ2: 0.589 / % possible all: 99.7

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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: 1UEI

1uei


Resolution: 2.424→46.583 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 2000 6.71 %
Rwork0.1888 --
obs0.1914 29824 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.424→46.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 100 145 3531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033432
X-RAY DIFFRACTIONf_angle_d0.5174639
X-RAY DIFFRACTIONf_dihedral_angle_d4.8492034
X-RAY DIFFRACTIONf_chiral_restr0.043540
X-RAY DIFFRACTIONf_plane_restr0.003584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4239-2.48450.31791160.27121601X-RAY DIFFRACTION80
2.4845-2.55170.29571440.24532005X-RAY DIFFRACTION100
2.5517-2.62680.26511410.22751981X-RAY DIFFRACTION100
2.6268-2.71150.26421440.22561992X-RAY DIFFRACTION100
2.7115-2.80840.2591440.22332007X-RAY DIFFRACTION100
2.8084-2.92090.27921430.23171995X-RAY DIFFRACTION100
2.9209-3.05380.28641440.22981994X-RAY DIFFRACTION100
3.0538-3.21470.26871450.21422020X-RAY DIFFRACTION100
3.2147-3.41610.25661430.20631990X-RAY DIFFRACTION100
3.4161-3.67980.22741460.1792024X-RAY DIFFRACTION100
3.6798-4.04990.19421440.17412009X-RAY DIFFRACTION100
4.0499-4.63550.20521460.14822045X-RAY DIFFRACTION100
4.6355-5.83840.21721470.17412040X-RAY DIFFRACTION100
5.8384-46.59170.18761530.18112121X-RAY DIFFRACTION99

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