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- PDB-2uvq: Crystal structure of human uridine-cytidine kinase 1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 2uvq
TitleCrystal structure of human uridine-cytidine kinase 1 in complex with ADP
ComponentsURIDINE-CYTIDINE KINASE 1
KeywordsTRANSFERASE / UCK / KINASE / ATP-BINDING / NUCLEOSIDE KINASE / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


uridine/cytidine kinase / CTP salvage / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / phosphorylation / ATP 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
ADENOSINE-5'-DIPHOSPHATE / Uridine-cytidine kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKosinska, U. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. ...Kosinska, U. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E.P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Uppsten, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P.
CitationJournal: To be Published
Title: Structure of Human Uridine-Cytidine Kinase 1
Authors: Kosinska, U. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B. ...Authors: Kosinska, U. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E.P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Uppsten, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P.
History
DepositionMar 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: URIDINE-CYTIDINE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6712
Polymers28,2441
Non-polymers4271
Water27015
1
A: URIDINE-CYTIDINE KINASE 1
hetero molecules

A: URIDINE-CYTIDINE KINASE 1
hetero molecules

A: URIDINE-CYTIDINE KINASE 1
hetero molecules

A: URIDINE-CYTIDINE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6868
Polymers112,9774
Non-polymers1,7094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_444-y-1,-x-1,-z-1/31
MethodPQS
Unit cell
Length a, b, c (Å)67.919, 67.919, 236.607
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein URIDINE-CYTIDINE KINASE 1 / UCK 1 / URIDINE MONOPHOSPHOKINASE 1 / CYTIDINE MONOPHOSPHOKINASE 1


Mass: 28244.295 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HA47, uridine/cytidine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growDetails: 0.8-1.0 M SUCCINIC ACID PH 6.7-7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2006 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3→29.4 Å / Num. obs: 12509 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 12.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.7
Reflection shellResolution: 3→3.16 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XRJ

1xrj


Resolution: 3→29.41 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 35.166 / SU ML: 0.308 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 330 4.7 %RANDOM
Rwork0.194 ---
obs0.197 6704 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.41 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 27 15 1734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221751
X-RAY DIFFRACTIONr_bond_other_d0.0010.021181
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.9842375
X-RAY DIFFRACTIONr_angle_other_deg0.85132871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65723.8184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8715306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9541514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_nbd_refined0.2090.2397
X-RAY DIFFRACTIONr_nbd_other0.1880.21239
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2859
X-RAY DIFFRACTIONr_nbtor_other0.0850.2979
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.70721369
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89131710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2664807
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8925665
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 23
Rwork0.253 482
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7399-0.2172-1.35991.1940.262.7742-0.0156-0.13070.17070.146-0.1859-0.1685-0.37280.45380.20160.0954-0.003-0.07610.64280.02810.43124.376-24.143-20.215
25.19773.0335-6.25647.69721.098112.7248-0.0795-0.40910.907-0.84530.4625-0.0761-1.62271.1451-0.3830.1602-0.1256-0.07590.80940.01470.602812.278-19.683-18.06
33.3730.79111.00932.40580.446110.3708-0.1921-0.4768-0.1632-0.13180.2213-0.09320.28410.3294-0.0292-0.04250.0506-0.00610.4120.02910.3729-4.472-28.576-23.897
47.5349-1.5124-1.61295.1491-1.0581.0256-0.2772-0.01541.26150.88140.4317-1.9478-1.251.2334-0.15460.6018-0.2272-0.24990.8730.18990.86241.174-13.578-38.175
55.0239-0.5873-3.20061.7232.03829.25970.1296-0.30990.14910.0722-0.17490.04720.2981-0.11580.0453-0.0291-0.011-0.0540.4426-0.02210.3133-11.281-27.369-19.383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 108
2X-RAY DIFFRACTION2A109 - 132
3X-RAY DIFFRACTION3A133 - 168
4X-RAY DIFFRACTION4A169 - 193
5X-RAY DIFFRACTION5A194 - 235

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