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- PDB-2qro: Human Deoxycytidine kinase dAMP, UDP, Mg ion product complex -

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Basic information

Entry
Database: PDB / ID: 2qro
TitleHuman Deoxycytidine kinase dAMP, UDP, Mg ion product complex
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / deoxycytidine kinase / deoxyadenosine monophosphate / uridine diphosphate / ATP-binding / Nucleotide-binding / Nucleus / Phosphorylation
Function / homology
Function and homology information


deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity ...deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity / pyrimidine nucleotide metabolic process / Purine salvage / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Deoxynucleoside kinase / : / Deoxynucleoside kinase domain / Deoxynucleoside kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsEalick, S.E. / Soriano, E.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structures of human deoxycytidine kinase product complexes.
Authors: Soriano, E.V. / Clark, V.C. / Ealick, S.E.
History
DepositionJul 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: Deoxycytidine kinase
B: Deoxycytidine kinase
C: Deoxycytidine kinase
D: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,93416
Polymers130,8954
Non-polymers3,03912
Water00
1
A: Deoxycytidine kinase
B: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9678
Polymers65,4482
Non-polymers1,5196
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
MethodPISA
2
C: Deoxycytidine kinase
D: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9678
Polymers65,4482
Non-polymers1,5196
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.688, 93.688, 332.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Deoxycytidine kinase / dCK


Mass: 32723.850 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Production host: Escherichia coli (E. coli) / References: UniProt: P27707, deoxycytidine kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O6P

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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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16-17% ethanol, 8% glycerol, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.45→38.6 Å / Num. all: 18290 / Num. obs: 17685 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 13.6
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.446 / % possible all: 89

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P60.pdb

1p60


Resolution: 3.45→38.6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 35411.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 935 5.3 %RANDOM
Rwork0.2 ---
all0.2 18290 --
obs0.2 17685 86.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.7 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 82.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.2 Å20 Å20 Å2
2--8.2 Å20 Å2
3----16.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.45→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7624 0 192 0 7816
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d2.36
X-RAY DIFFRACTIONc_mcbond_it9.821.5
X-RAY DIFFRACTIONc_mcangle_it15.242
X-RAY DIFFRACTIONc_scbond_it14.552
X-RAY DIFFRACTIONc_scangle_it20.832.5
LS refinement shellResolution: 3.45→3.67 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 166 5.9 %
Rwork0.257 2644 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3udp.paramudp.top
X-RAY DIFFRACTION4da.paramda.top

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