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

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Basic information

Entry
Database: PDB / ID: 1uei
TitleCrystal structure of human uridine-cytidine kinase 2 complexed with a feedback-inhibitor, UTP
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 / UMP salvage / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Uridine-cytidine kinase 2 / Uridine kinase-like / Phosphoribulokinase / Uridine kinase family / Phosphoribulokinase/uridine kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / Uridine-cytidine kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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

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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)57,4944
Polymers56,5262
Non-polymers9682
Water1,62190
1
A: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7472
Polymers28,2631
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7472
Polymers28,2631
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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)114,9898
Polymers113,0524
Non-polymers1,9374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+1/2,y,-z+1/21
Buried area8700 Å2
ΔGint-35 kcal/mol
Surface area34250 Å2
MethodPISA
4
A: Uridine-cytidine kinase 2
hetero molecules

B: Uridine-cytidine kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4944
Polymers56,5262
Non-polymers9682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+1/2,y,-z+1/21
Buried area2870 Å2
ΔGint-12 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.529, 247.748, 91.673
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-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.95 Å3/Da / Density % sol: 68.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: sodium tartrate, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD / Detector: CCD / Date: May 27, 2002
RadiationMonochromator: rotated-inclined monochromator and vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→39.1 Å / Num. all: 19587 / Num. obs: 19587 / % possible obs: 84.3 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.2 / % possible all: 86.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UDW
Resolution: 2.6→39.06 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 350363.52 / 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
Rfree0.245 1898 9.8 %RANDOM
Rwork0.204 ---
all0.208 19277 --
obs0.204 19277 82.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.8496 Å2 / ksol: 0.376614 e/Å3
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1-12.07 Å20 Å20 Å2
2---12.26 Å20 Å2
3---0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 58 90 3376
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 316 9.9 %
Rwork0.259 2888 -
obs-3204 83.7 %
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 DIFFRACTION5UTP.PARAMUTP.TOP

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