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- PDB-1uej: Crystal structure of human uridine-cytidine kinase 2 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1uej
TitleCrystal structure of human uridine-cytidine kinase 2 complexed with a substrate, cytidine
ComponentsUridine-cytidine kinase 2
KeywordsTRANSFERASE / ALPHA/BETA MONONUCLEOTIDE-BINDING HOLD
Function / homology
Function and homology information


uridine/cytidine kinase / CTP salvage / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / phosphorylation / 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
CITRIC ACID / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / Uridine-cytidine kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsSuzuki, N.N. / Koizumi, K. / Fukushima, M. / Matsuda, A. / Inagaki, F.
Citation
Journal: STRUCTURE / Year: 2004
Title: Structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase
Authors: Suzuki, N.N. / Koizumi, K. / Fukushima, M. / Matsuda, A. / Inagaki, F.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Crystallization and preliminary X-ray analysis of human uridine-cytidine kinase 2
Authors: Suzuki, N.N. / Koizumi, K. / Fukushima, M. / Matsuda, A. / Inagaki, F.
History
DepositionMay 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3976
Polymers56,5262
Non-polymers8714
Water1,49583
1
A: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6983
Polymers28,2631
Non-polymers4352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6983
Polymers28,2631
Non-polymers4352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.296, 247.631, 90.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Uridine-cytidine kinase 2 / URIDINE-CYTIDINE KINASE


Mass: 28262.994 Da / Num. of mol.: 2 / Fragment: residues 1-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9BZX2, uridine/cytidine kinase
#2: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE / Cytidine


Mass: 243.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O5
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 4.11 Å3/Da / Density % sol: 69.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: sodium citrate, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 23533 / Num. obs: 23533 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.27 / Num. unique all: 2358 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UDW

1udw


Resolution: 2.61→37.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 982277.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2096 9.9 %RANDOM
Rwork0.213 ---
all0.217 21186 --
obs0.213 21186 88.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.4696 Å2 / ksol: 0.374115 e/Å3
Displacement parametersBiso mean: 48.8 Å2
Baniso -1Baniso -2Baniso -3
1-29.2 Å20 Å20 Å2
2---21.29 Å20 Å2
3----7.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.61→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 60 83 3385
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 293 10.1 %
Rwork0.321 2604 -
obs-2897 72.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CYDCIT.PARAMCYDCIT.TOP

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